rs74879986

Variant names:

• chr4-31154556-G-A
• rs74879986

Your query was ambiguous. Multiple possible variants found:

• chr4-31154556-G-A
• chr4-31154556-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0267 in 152,124 control chromosomes in the GnomAD database, including 92 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 0.027 (92 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0267 (4069/152124) while in subpopulation AMR AF = 0.0407 (621/15240). AF 95% confidence interval is 0.0381. There are 92 homozygotes in GnomAd4. There are 1978 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 92 gene

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: 0.0267 AC: 4058 AN: 152006 Hom.: 91 Cov.: 31

Gnomad AFR AF: 0.00860

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0407

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0350

Gnomad OTH AF: 0.0451

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

GnomAD4 genome AF: 0.0267 AC: 4069 AN: 152124 Hom.: 92 Cov.: 31 AF XY: 0.0266 AC XY: 1978 AN XY: 74362

African (AFR) AF: 0.00886 AC: 368 AN: 41518

American (AMR) AF: 0.0407 AC: 621 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0469 AC: 163 AN: 3472

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5170

South Asian (SAS) AF: 0.0257 AC: 124 AN: 4816

European-Finnish (FIN) AF: 0.0256 AC: 272 AN: 10606

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0350 AC: 2380 AN: 67992

Other (OTH) AF: 0.0442 AC: 93 AN: 2106

Alfa AF: 0.00394 Hom.: 3

Bravo AF: 0.0283

Asia WGS AF: 0.0200 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.36
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs74879986; hg19: chr4-31156178;