rs4691651

Variant names:

• chr4-160414452-T-C
• rs4691651

Your query was ambiguous. Multiple possible variants found:

• chr4-160414452-T-C
• chr4-160414452-T-G

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 0.0206 in 152,292 control chromosomes in the GnomAD database, including 47 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 0.021 (47 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.058 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: 0.0206 AC: 3129 AN: 152174 Hom.: 48 Cov.: 33

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.0634

Gnomad SAS AF: 0.0130

Gnomad FIN AF: 0.0244

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00412

Gnomad OTH AF: 0.0296

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

GnomAD4 genome AF: 0.0206 AC: 3133 AN: 152292 Hom.: 47 Cov.: 33 AF XY: 0.0218 AC XY: 1624 AN XY: 74466

African (AFR) AF: 0.0367 AC: 1526 AN: 41556

American (AMR) AF: 0.0375 AC: 574 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00720 AC: 25 AN: 3470

East Asian (EAS) AF: 0.0637 AC: 330 AN: 5180

South Asian (SAS) AF: 0.0128 AC: 62 AN: 4826

European-Finnish (FIN) AF: 0.0244 AC: 259 AN: 10614

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00409 AC: 278 AN: 68030

Other (OTH) AF: 0.0298 AC: 63 AN: 2114

Alfa AF: 0.00670 Hom.: 3

Bravo AF: 0.0231

Asia WGS AF: 0.0510 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.9
DANN	Benign	0.74
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs4691651; hg19: chr4-161335604;