rs4708388

Variant names:

• chr6-168893570-G-A
• rs4708388

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 0.13 in 152,022 control chromosomes in the GnomAD database, including 1,439 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 0.13 (1439 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.620
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 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: 0.130 AC: 19779 AN: 151904 Hom.: 1434 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.130 AC: 19797 AN: 152022 Hom.: 1439 Cov.: 33 AF XY: 0.135 AC XY: 10028 AN XY: 74302

African (AFR) AF: 0.120 AC: 4977 AN: 41454

American (AMR) AF: 0.152 AC: 2327 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0885 AC: 307 AN: 3468

East Asian (EAS) AF: 0.298 AC: 1540 AN: 5174

South Asian (SAS) AF: 0.201 AC: 967 AN: 4814

European-Finnish (FIN) AF: 0.151 AC: 1597 AN: 10548

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7593 AN: 67982

Other (OTH) AF: 0.130 AC: 275 AN: 2108

Alfa AF: 0.116 Hom.: 507

Bravo AF: 0.128

Asia WGS AF: 0.255 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.71
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs4708388; hg19: chr6-169293665; COSMIC: COSV60304690;