3-7869340-G-C

Variant names:

• chr3-7869340-G-C
• rs10510373

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 0.0883 in 152,046 control chromosomes in the GnomAD database, including 682 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 0.088 (682 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 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: 0.0883 AC: 13409 AN: 151928 Hom.: 681 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.0648

Gnomad ASJ AF: 0.0675

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.0741

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0909

Gnomad OTH AF: 0.0879

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

GnomAD4 genome AF: 0.0883 AC: 13422 AN: 152046 Hom.: 682 Cov.: 31 AF XY: 0.0846 AC XY: 6288 AN XY: 74368

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.0648

Gnomad4 ASJ AF: 0.0675

Gnomad4 EAS AF: 0.0159

Gnomad4 SAS AF: 0.0432

Gnomad4 FIN AF: 0.0741

Gnomad4 NFE AF: 0.0908

Gnomad4 OTH AF: 0.0875

Alfa AF: 0.0913 Hom.: 85

Bravo AF: 0.0892

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.81
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510373; hg19: chr3-7911027;