rs1610302

Variant names:

• chr20-2215913-G-C
• rs1610302
• ENST00000651531.1:c.-49+8394G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651531.1(ENSG00000286022):​c.-49+8394G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,030 control chromosomes in the GnomAD database, including 7,431 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 0.28 (7431 hom., cov: 32)
• Consequence: ENSG00000286022 ENST00000651531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 2 publications found

Genes affected

ENSG00000286022 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286022	ENST00000651531.1	c.-49+8394G>C		intron_variant	Intron 1 of 13			ENSP00000498584.1

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43191 AN: 151910 Hom.: 7421 Cov.: 32

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.284 AC: 43206 AN: 152030 Hom.: 7431 Cov.: 32 AF XY: 0.289 AC XY: 21456 AN XY: 74298

African (AFR) AF: 0.0860 AC: 3572 AN: 41524

American (AMR) AF: 0.407 AC: 6206 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1147 AN: 3470

East Asian (EAS) AF: 0.469 AC: 2420 AN: 5160

South Asian (SAS) AF: 0.368 AC: 1771 AN: 4818

European-Finnish (FIN) AF: 0.309 AC: 3256 AN: 10546

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23697 AN: 67940

Other (OTH) AF: 0.318 AC: 672 AN: 2110

Alfa AF: 0.312 Hom.: 1023

Bravo AF: 0.285

Asia WGS AF: 0.400 AC: 1389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.089
DANN	Benign	0.44
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1610302; hg19: chr20-2196559;