4-73921168-T-C

Variant names:

• chr4-73921168-T-C
• rs2117721

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 0.783 in 152,194 control chromosomes in the GnomAD database, including 49,048 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 0.78 (49048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 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: 0.784 AC: 119170 AN: 152076 Hom.: 49044 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.783 AC: 119212 AN: 152194 Hom.: 49048 Cov.: 32 AF XY: 0.787 AC XY: 58534 AN XY: 74406

African (AFR) AF: 0.505 AC: 20975 AN: 41512

American (AMR) AF: 0.885 AC: 13530 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3110 AN: 3470

East Asian (EAS) AF: 0.977 AC: 5068 AN: 5186

South Asian (SAS) AF: 0.814 AC: 3927 AN: 4822

European-Finnish (FIN) AF: 0.885 AC: 9388 AN: 10606

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60372 AN: 67984

Other (OTH) AF: 0.811 AC: 1714 AN: 2114

Alfa AF: 0.784 Hom.: 2994

Bravo AF: 0.772

Asia WGS AF: 0.831 AC: 2883 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.20
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2117721; hg19: chr4-74786885;