4-73921168-T-C

Variant names:

• chr4-73921168-T-C
• rs2117721

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.811

Alfa AF: 0.807 Hom.: 2886

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2117721; hg19: chr4-74786885;