rs6811287

Positions:

• chr4-10179199-C-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 0.425 in 151,966 control chromosomes in the GnomAD database, including 13,938 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 0.42 (13938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

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 (SAS) allele frequency at 95% confidence interval = 0.61 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: 0.424 AC: 64453 AN: 151848 Hom.: 13919 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.425 AC: 64510 AN: 151966 Hom.: 13938 Cov.: 32 AF XY: 0.429 AC XY: 31844 AN XY: 74278

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.427

Alfa AF: 0.444 Hom.: 25420

Bravo AF: 0.417

Asia WGS AF: 0.538 AC: 1865 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.14
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6811287; hg19: chr4-10180823;