rs10264893

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;