6-34578783-C-T

Variant names:

• chr6-34578783-C-T
• rs2814982

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 0.155 in 152,080 control chromosomes in the GnomAD database, including 2,313 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 0.16 (2313 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608
• Publications: 67 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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: 0.155 AC: 23630 AN: 151962 Hom.: 2315 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0762

Gnomad SAS AF: 0.0722

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.155 AC: 23636 AN: 152080 Hom.: 2313 Cov.: 31 AF XY: 0.155 AC XY: 11545 AN XY: 74344

African (AFR) AF: 0.274 AC: 11340 AN: 41444

American (AMR) AF: 0.0911 AC: 1393 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3472

East Asian (EAS) AF: 0.0758 AC: 393 AN: 5182

South Asian (SAS) AF: 0.0713 AC: 343 AN: 4814

European-Finnish (FIN) AF: 0.176 AC: 1856 AN: 10574

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7585 AN: 67984

Other (OTH) AF: 0.135 AC: 285 AN: 2110

Alfa AF: 0.118 Hom.: 5768

Bravo AF: 0.153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.51
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs2814982; hg19: chr6-34546560;