rs10498077

Positions:

• chr2-220374193-T-C

Variant summary

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

The ENST00000432993.1(ENSG00000239498):​n.427+51972T>C 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 0.0497 in 152,220 control chromosomes in the GnomAD database, including 491 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 0.050 (491 hom., cov: 32)
• Consequence: ENST00000432993.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373893	XR_001739889.2	n.394+51972T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000432993.1	n.427+51972T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0495 AC: 7530 AN: 152102 Hom.: 484 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0235

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.00496

Gnomad FIN AF: 0.00528

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00795

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0497 AC: 7568 AN: 152220 Hom.: 491 Cov.: 32 AF XY: 0.0493 AC XY: 3671 AN XY: 74414

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.0234

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.00476

Gnomad4 FIN AF: 0.00528

Gnomad4 NFE AF: 0.00795

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0369 Hom.: 39

Bravo AF: 0.0557

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498077; hg19: chr2-221238914;