rs10264893

Variant names:

• chr7-104013977-G-A
• rs10264893

Your query was ambiguous. Multiple possible variants found:

• chr7-104013977-G-A
• chr7-104013977-G-T

Variant summary

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

The variant allele was found at a frequency of 0.475 in 151,946 control chromosomes in the GnomAD database, including 17,488 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 0.48 (17488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 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

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72166 AN: 151828 Hom.: 17480 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.475 AC: 72215 AN: 151946 Hom.: 17488 Cov.: 32 AF XY: 0.485 AC XY: 36055 AN XY: 74268

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.487

Alfa AF: 0.428 Hom.: 7247

Bravo AF: 0.472

Asia WGS AF: 0.601 AC: 2094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10264893; hg19: chr7-103654424;