rs6904071

Variant names:

• chr6-27079477-G-A
• rs6904071

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 0.138 in 152,068 control chromosomes in the GnomAD database, including 1,595 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 0.14 (1595 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• Publications: 39 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 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: 0.139 AC: 21050 AN: 151950 Hom.: 1595 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.00886

Gnomad SAS AF: 0.0936

Gnomad FIN AF: 0.0905

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.138 AC: 21051 AN: 152068 Hom.: 1595 Cov.: 32 AF XY: 0.132 AC XY: 9813 AN XY: 74358

African (AFR) AF: 0.137 AC: 5700 AN: 41460

American (AMR) AF: 0.106 AC: 1612 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3468

East Asian (EAS) AF: 0.00888 AC: 46 AN: 5182

South Asian (SAS) AF: 0.0922 AC: 445 AN: 4824

European-Finnish (FIN) AF: 0.0905 AC: 958 AN: 10584

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11525 AN: 67960

Other (OTH) AF: 0.123 AC: 259 AN: 2114

Alfa AF: 0.157 Hom.: 6380

Bravo AF: 0.140

Asia WGS AF: 0.0590 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.69
DANN	Benign	0.44
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs6904071; hg19: chr6-27047256;