rs10503701

Variant names:

• chr8-21262649-G-C
• rs10503701
• ENST00000657734.1:n.1326+32485C>G

Variant summary

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

The ENST00000657734.1(ENSG00000254092):​n.1326+32485C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0507 in 152,188 control chromosomes in the GnomAD database, including 509 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 0.051 (509 hom., cov: 32)
• Consequence: ENSG00000254092 ENST00000657734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

Genes affected

ENSG00000254092 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254092	ENST00000657734.1	n.1326+32485C>G		intron_variant	Intron 2 of 4
ENSG00000254092	ENST00000659453.1	n.1639+32485C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0507 AC: 7705 AN: 152070 Hom.: 508 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0269

Gnomad ASJ AF: 0.0468

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00914

Gnomad FIN AF: 0.000565

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.00690

Gnomad OTH AF: 0.0513

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

GnomAD4 genome AF: 0.0507 AC: 7721 AN: 152188 Hom.: 509 Cov.: 32 AF XY: 0.0480 AC XY: 3575 AN XY: 74410

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.0269

Gnomad4 ASJ AF: 0.0468

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00936

Gnomad4 FIN AF: 0.000565

Gnomad4 NFE AF: 0.00690

Gnomad4 OTH AF: 0.0508

Alfa AF: 0.0316 Hom.: 34

Bravo AF: 0.0579

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503701; hg19: chr8-21120160;