rs2331564

Variant names:

• chr4-68964336-C-G
• rs2331564

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.206 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

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.203

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2331564; hg19: chr4-69830054;