10-102902701-T-C

Variant names:

• chr10-102902701-T-C
• rs7897654
• ENST00000652934.1:n.169-2191A>G

Variant summary

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

The ENST00000652934.1(ENSG00000286575):​n.169-2191A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,062 control chromosomes in the GnomAD database, including 7,066 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 0.30 (7066 hom., cov: 32)
• Consequence: ENSG00000286575 ENST00000652934.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 24 publications found

Genes affected

ENSG00000286575 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984265	NR_160733.1	n.169-2191A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286575	ENST00000652934.1	n.169-2191A>G		intron_variant	Intron 1 of 2
ENSG00000286575	ENST00000769603.1	n.412-2191A>G		intron_variant	Intron 1 of 2
ENSG00000286575	ENST00000769604.1	n.279-2191A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45468 AN: 151944 Hom.: 7058 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.299 AC: 45512 AN: 152062 Hom.: 7066 Cov.: 32 AF XY: 0.298 AC XY: 22142 AN XY: 74332

African (AFR) AF: 0.257 AC: 10660 AN: 41476

American (AMR) AF: 0.281 AC: 4285 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3468

East Asian (EAS) AF: 0.471 AC: 2442 AN: 5180

South Asian (SAS) AF: 0.357 AC: 1721 AN: 4822

European-Finnish (FIN) AF: 0.295 AC: 3113 AN: 10552

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21248 AN: 67980

Other (OTH) AF: 0.313 AC: 660 AN: 2110

Alfa AF: 0.304 Hom.: 11727

Bravo AF: 0.295

Asia WGS AF: 0.369 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.75
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs7897654; hg19: chr10-104662458; COSMIC: COSV54915911;