chr4-81009660-C-T

Variant names:

• chr4-81009660-C-T
• rs1960445

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 0.816 in 152,260 control chromosomes in the GnomAD database, including 51,899 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 0.82 (51899 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 12 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 (EAS) allele frequency at 95% confidence interval = 0.918 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: 0.816 AC: 124222 AN: 152142 Hom.: 51870 Cov.: 34

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.816 AC: 124297 AN: 152260 Hom.: 51899 Cov.: 34 AF XY: 0.820 AC XY: 61077 AN XY: 74452

African (AFR) AF: 0.628 AC: 26055 AN: 41518

American (AMR) AF: 0.875 AC: 13398 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2498 AN: 3472

East Asian (EAS) AF: 0.940 AC: 4867 AN: 5176

South Asian (SAS) AF: 0.870 AC: 4202 AN: 4828

European-Finnish (FIN) AF: 0.918 AC: 9742 AN: 10610

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.893 AC: 60780 AN: 68032

Other (OTH) AF: 0.818 AC: 1731 AN: 2116

Alfa AF: 0.838 Hom.: 17408

Bravo AF: 0.804

Asia WGS AF: 0.886 AC: 3081 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	0.27
DANN	Benign	0.23
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs1960445; hg19: chr4-81930814;