rs7683465

Variant names:

• chr4-108302381-G-A
• rs7683465

Your query was ambiguous. Multiple possible variants found:

• chr4-108302381-G-A
• chr4-108302381-G-C
• chr4-108302381-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 0.583 in 152,062 control chromosomes in the GnomAD database, including 28,457 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 0.58 (28457 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670

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 (EAS) allele frequency at 95% confidence interval = 0.807 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: 0.583 AC: 88627 AN: 151944 Hom.: 28441 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.583 AC: 88655 AN: 152062 Hom.: 28457 Cov.: 32 AF XY: 0.589 AC XY: 43739 AN XY: 74312

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.625

Alfa AF: 0.600 Hom.: 4228

Bravo AF: 0.576

Asia WGS AF: 0.758 AC: 2637 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	1.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7683465; hg19: chr4-109223537;