rs6820756

Positions:

• chr4-10061225-A-G
• chr4-10061225-A-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 0.741 in 152,178 control chromosomes in the GnomAD database, including 42,222 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 0.74 (42222 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 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: 0.741 AC: 112685 AN: 152060 Hom.: 42195 Cov.: 33

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.741 AC: 112752 AN: 152178 Hom.: 42222 Cov.: 33 AF XY: 0.735 AC XY: 54702 AN XY: 74402

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.737

Alfa AF: 0.768 Hom.: 53492

Bravo AF: 0.728

Asia WGS AF: 0.636 AC: 2215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.27
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6820756; hg19: chr4-10062849;