6-35557100-A-T

Variant names:

• chr6-35557100-A-T
• rs873941

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 0.704 in 151,802 control chromosomes in the GnomAD database, including 37,835 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 0.70 (37835 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 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: 0.704 AC: 106810 AN: 151684 Hom.: 37790 Cov.: 33

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.704 AC: 106913 AN: 151802 Hom.: 37835 Cov.: 33 AF XY: 0.707 AC XY: 52435 AN XY: 74190

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.668

Alfa AF: 0.621 Hom.: 1905

Bravo AF: 0.706

Asia WGS AF: 0.774 AC: 2690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs873941; hg19: chr6-35524877;