rs7683465

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;