rs4708818

Variant names:

• chr6-159302471-C-G
• rs4708818

Your query was ambiguous. Multiple possible variants found:

• chr6-159302471-C-G
• chr6-159302471-C-T

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 0.535 in 152,056 control chromosomes in the GnomAD database, including 25,018 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 0.54 (25018 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447
• Publications: 4 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 = 0.676 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: 0.535 AC: 81360 AN: 151938 Hom.: 25020 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.535 AC: 81362 AN: 152056 Hom.: 25018 Cov.: 32 AF XY: 0.536 AC XY: 39870 AN XY: 74346

African (AFR) AF: 0.228 AC: 9466 AN: 41442

American (AMR) AF: 0.632 AC: 9656 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2311 AN: 3472

East Asian (EAS) AF: 0.295 AC: 1522 AN: 5160

South Asian (SAS) AF: 0.557 AC: 2683 AN: 4820

European-Finnish (FIN) AF: 0.694 AC: 7339 AN: 10578

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.682 AC: 46335 AN: 67980

Other (OTH) AF: 0.588 AC: 1241 AN: 2110

Alfa AF: 0.592 Hom.: 3469

Bravo AF: 0.517

Asia WGS AF: 0.426 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.81
DANN	Benign	0.47
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs4708818; hg19: chr6-159723503; COSMIC: COSV60298415;