chr6-7106083-G-C

Variant names:

• chr6-7106083-G-C
• rs2842895

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.394 in 152,134 control chromosomes in the GnomAD database, including 15,445 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 0.39 (15445 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.18
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.56 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: 0.394 AC: 59951 AN: 152016 Hom.: 15450 Cov.: 32

Gnomad AFR AF: 0.0982

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.00674

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.394 AC: 59942 AN: 152134 Hom.: 15445 Cov.: 32 AF XY: 0.392 AC XY: 29141 AN XY: 74352

African (AFR) AF: 0.0979 AC: 4065 AN: 41534

American (AMR) AF: 0.454 AC: 6937 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1753 AN: 3466

East Asian (EAS) AF: 0.00694 AC: 36 AN: 5184

South Asian (SAS) AF: 0.287 AC: 1382 AN: 4818

European-Finnish (FIN) AF: 0.533 AC: 5619 AN: 10538

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.565 AC: 38399 AN: 67996

Other (OTH) AF: 0.449 AC: 949 AN: 2114

Alfa AF: 0.473 Hom.: 2390

Bravo AF: 0.373

Asia WGS AF: 0.135 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	22
DANN	Benign	0.71
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs2842895; hg19: chr6-7106316;