rs6838905

Variant names:

• chr4-38710665-A-G
• rs6838905

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 0.115 in 152,196 control chromosomes in the GnomAD database, including 1,013 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 0.12 (1013 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 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: 0.115 AC: 17515 AN: 152078 Hom.: 1013 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0751

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.00326

Gnomad SAS AF: 0.0674

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.115 AC: 17523 AN: 152196 Hom.: 1013 Cov.: 32 AF XY: 0.112 AC XY: 8326 AN XY: 74434

African (AFR) AF: 0.115 AC: 4771 AN: 41544

American (AMR) AF: 0.0750 AC: 1146 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0983 AC: 341 AN: 3468

East Asian (EAS) AF: 0.00327 AC: 17 AN: 5196

South Asian (SAS) AF: 0.0673 AC: 325 AN: 4830

European-Finnish (FIN) AF: 0.135 AC: 1426 AN: 10566

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9091 AN: 67988

Other (OTH) AF: 0.110 AC: 233 AN: 2110

Alfa AF: 0.124 Hom.: 1434

Bravo AF: 0.111

Asia WGS AF: 0.0480 AC: 167 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.2
DANN	Benign	0.89
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs6838905; hg19: chr4-38712286;