rs1999774

Positions:

• chr10-44585946-T-A
• chr10-44585946-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007062357.1(LOC124902533):​n.871-4667T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,012 control chromosomes in the GnomAD database, including 13,178 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 0.39 (13178 hom., cov: 32)
• Consequence: LOC124902533 XR_007062357.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

LOC124902533 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902533	XR_007062357.1	n.871-4667T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58966 AN: 151894 Hom.: 13164 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.406

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.388 AC: 59015 AN: 152012 Hom.: 13178 Cov.: 32 AF XY: 0.392 AC XY: 29159 AN XY: 74296

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.411

Alfa AF: 0.301 Hom.: 859

Bravo AF: 0.379

Asia WGS AF: 0.485 AC: 1689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1999774; hg19: chr10-45081394;