22-50149702-C-T

Variant names:

• chr22-50149702-C-T
• rs138271
• NM_018995.3:c.2715C>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_018995.3(MOV10L1):​c.2715C>T​(p.Asp905Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,612,424 control chromosomes in the GnomAD database, including 74,670 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.23 (5067 hom., cov: 33)
  • Exomes 𝑓: 0.30 (69603 hom.)
• Consequence: MOV10L1 NM_018995.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 17 publications found

Genes affected

MOV10L1 (HGNC:7201): (Mov10 like RNA helicase 1) This gene is similar to a mouse gene that encodes a putative RNA helicase and shows testis-specific expression. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP7: Synonymous conserved (PhyloP=0.342 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOV10L1	NM_018995.3	c.2715C>T	p.Asp905Asp	synonymous_variant	Exon 20 of 27	ENST00000262794.10	NP_061868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOV10L1	ENST00000262794.10	c.2715C>T	p.Asp905Asp	synonymous_variant	Exon 20 of 27	1	NM_018995.3	ENSP00000262794.5

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35418 AN: 152074 Hom.: 5070 Cov.: 33

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.00674

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.207

GnomAD2 exomes AF: 0.243 AC: 60428 AN: 249112 AF XY: 0.247

Gnomad AFR exome AF: 0.0827

Gnomad AMR exome AF: 0.182

Gnomad ASJ exome AF: 0.220

Gnomad EAS exome AF: 0.00541

Gnomad FIN exome AF: 0.345

Gnomad NFE exome AF: 0.318

Gnomad OTH exome AF: 0.251

GnomAD4 exome AF: 0.299 AC: 436065 AN: 1460232 Hom.: 69603 Cov.: 34 AF XY: 0.296 AC XY: 214925 AN XY: 726342

African (AFR) AF: 0.0754 AC: 2523 AN: 33464

American (AMR) AF: 0.186 AC: 8284 AN: 44604

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 5753 AN: 26106

East Asian (EAS) AF: 0.00343 AC: 136 AN: 39640

South Asian (SAS) AF: 0.196 AC: 16914 AN: 86084

European-Finnish (FIN) AF: 0.345 AC: 18381 AN: 53338

Middle Eastern (MID) AF: 0.200 AC: 1142 AN: 5720

European-Non Finnish (NFE) AF: 0.330 AC: 366580 AN: 1110920

Other (OTH) AF: 0.271 AC: 16352 AN: 60356

GnomAD4 genome AF: 0.233 AC: 35417 AN: 152192 Hom.: 5067 Cov.: 33 AF XY: 0.233 AC XY: 17318 AN XY: 74404

African (AFR) AF: 0.0858 AC: 3564 AN: 41560

American (AMR) AF: 0.235 AC: 3589 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 756 AN: 3470

East Asian (EAS) AF: 0.00676 AC: 35 AN: 5178

South Asian (SAS) AF: 0.188 AC: 907 AN: 4824

European-Finnish (FIN) AF: 0.353 AC: 3728 AN: 10558

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 21996 AN: 67992

Other (OTH) AF: 0.204 AC: 431 AN: 2110

Alfa AF: 0.287 Hom.: 11282

Bravo AF: 0.217

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.31
DANN	Benign	0.39
PhyloP100		0.34
PromoterAI		-0.0012	Neutral
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs138271; hg19: chr22-50588131; COSMIC: COSV53171624;