4-68964336-C-G

Variant names:

• chr4-68964336-C-G
• rs2331564

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 0.206 in 150,994 control chromosomes in the GnomAD database, including 3,684 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 0.21 (3684 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31067 AN: 150876 Hom.: 3677 Cov.: 29

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.206 AC: 31096 AN: 150994 Hom.: 3684 Cov.: 29 AF XY: 0.209 AC XY: 15406 AN XY: 73660

African (AFR) AF: 0.266 AC: 10915 AN: 41054

American (AMR) AF: 0.196 AC: 2976 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3460

East Asian (EAS) AF: 0.493 AC: 2504 AN: 5084

South Asian (SAS) AF: 0.273 AC: 1294 AN: 4744

European-Finnish (FIN) AF: 0.128 AC: 1341 AN: 10440

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10926 AN: 67740

Other (OTH) AF: 0.203 AC: 425 AN: 2096

Alfa AF: 0.178 Hom.: 311

Bravo AF: 0.215

Asia WGS AF: 0.340 AC: 1180 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.36
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2331564; hg19: chr4-69830054;