4-180967750-A-G

Variant names:

• chr4-180967750-A-G
• rs10018261

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 0.352 in 152,044 control chromosomes in the GnomAD database, including 9,612 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 0.35 (9612 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53458 AN: 151924 Hom.: 9606 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.352 AC: 53501 AN: 152044 Hom.: 9612 Cov.: 32 AF XY: 0.350 AC XY: 26003 AN XY: 74306

African (AFR) AF: 0.344 AC: 14245 AN: 41460

American (AMR) AF: 0.418 AC: 6393 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1532 AN: 3472

East Asian (EAS) AF: 0.188 AC: 969 AN: 5164

South Asian (SAS) AF: 0.183 AC: 881 AN: 4814

European-Finnish (FIN) AF: 0.375 AC: 3964 AN: 10568

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24282 AN: 67980

Other (OTH) AF: 0.381 AC: 802 AN: 2104

Alfa AF: 0.352 Hom.: 18096

Bravo AF: 0.357

Asia WGS AF: 0.196 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.72
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs10018261; hg19: chr4-181888903;