rs74879986

chr4-31154556-G-Achr4-31154556-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 91 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00886

Gnomad4 AMR AF: 0.0407

Gnomad4 ASJ AF: 0.0469

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0257

Gnomad4 FIN AF: 0.0256

Gnomad4 NFE AF: 0.0350

Gnomad4 OTH AF: 0.0442

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs74879986; hg19: chr4-31156178;