6-31039078-T-C

Variant names:

• chr6-31039078-T-C
• rs2844665

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.646 in 152,036 control chromosomes in the GnomAD database, including 32,013 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 0.65 (32013 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 33 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 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: 0.646 AC: 98197 AN: 151918 Hom.: 31978 Cov.: 31

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.646 AC: 98279 AN: 152036 Hom.: 32013 Cov.: 31 AF XY: 0.644 AC XY: 47817 AN XY: 74306

African (AFR) AF: 0.708 AC: 29365 AN: 41450

American (AMR) AF: 0.610 AC: 9326 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2797 AN: 3468

East Asian (EAS) AF: 0.490 AC: 2538 AN: 5178

South Asian (SAS) AF: 0.643 AC: 3096 AN: 4814

European-Finnish (FIN) AF: 0.620 AC: 6545 AN: 10558

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.623 AC: 42312 AN: 67962

Other (OTH) AF: 0.677 AC: 1429 AN: 2112

Alfa AF: 0.634 Hom.: 117344

Bravo AF: 0.650

Asia WGS AF: 0.635 AC: 2211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.34
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2844665; hg19: chr6-31006855;