chr4-156090771-G-T

Variant names:

• chr4-156090771-G-T
• rs10030044

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 0.606 in 151,824 control chromosomes in the GnomAD database, including 28,055 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 0.61 (28055 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.69 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: 0.606 AC: 91984 AN: 151704 Hom.: 28052 Cov.: 31

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.606 AC: 92024 AN: 151824 Hom.: 28055 Cov.: 31 AF XY: 0.614 AC XY: 45581 AN XY: 74180

African (AFR) AF: 0.551 AC: 22779 AN: 41372

American (AMR) AF: 0.655 AC: 9986 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2433 AN: 3466

East Asian (EAS) AF: 0.604 AC: 3102 AN: 5140

South Asian (SAS) AF: 0.709 AC: 3408 AN: 4804

European-Finnish (FIN) AF: 0.667 AC: 7019 AN: 10520

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41203 AN: 67954

Other (OTH) AF: 0.642 AC: 1356 AN: 2112

Alfa AF: 0.606 Hom.: 90572

Bravo AF: 0.598

Asia WGS AF: 0.662 AC: 2302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.010
DANN	Benign	0.39
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10030044; hg19: chr4-157011923;