6-4700910-G-T

Position:

• chr6-4700910-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 0.5 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;