6-4700910-G-T

Variant names:

• chr6-4700910-G-T
• rs4959312

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 0.5 in 150,662 control chromosomes in the GnomAD database, including 19,391 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 0.50 (19391 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.567 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: 0.500 AC: 75329 AN: 150554 Hom.: 19386 Cov.: 27

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.500 AC: 75368 AN: 150662 Hom.: 19391 Cov.: 27 AF XY: 0.504 AC XY: 37086 AN XY: 73542

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.501

Alfa AF: 0.534 Hom.: 37472

Bravo AF: 0.491

Asia WGS AF: 0.557 AC: 1936 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.14
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4959312; hg19: chr6-4701144;