rs4956211

Variant names:

• chr4-108801970-G-A
• rs4956211

Your query was ambiguous. Multiple possible variants found:

• chr4-108801970-G-A
• chr4-108801970-G-C

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 0.37 in 151,786 control chromosomes in the GnomAD database, including 10,463 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 0.37 (10463 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 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: 0.370 AC: 56169 AN: 151668 Hom.: 10459 Cov.: 31

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.370 AC: 56197 AN: 151786 Hom.: 10463 Cov.: 31 AF XY: 0.376 AC XY: 27907 AN XY: 74172

African (AFR) AF: 0.354 AC: 14645 AN: 41354

American (AMR) AF: 0.391 AC: 5968 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1229 AN: 3468

East Asian (EAS) AF: 0.266 AC: 1370 AN: 5150

South Asian (SAS) AF: 0.457 AC: 2198 AN: 4806

European-Finnish (FIN) AF: 0.445 AC: 4681 AN: 10530

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24787 AN: 67916

Other (OTH) AF: 0.378 AC: 796 AN: 2108

Alfa AF: 0.363 Hom.: 25285

Bravo AF: 0.362

Asia WGS AF: 0.383 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.85
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs4956211; hg19: chr4-109723126;