4-100980253-A-C

Variant names:

• chr4-100980253-A-C
• rs72927357

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 0.0257 in 152,312 control chromosomes in the GnomAD database, including 114 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 0.026 (114 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.22
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0634 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: 0.0256 AC: 3898 AN: 152194 Hom.: 113 Cov.: 32

Gnomad AFR AF: 0.0654

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0111

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0399

Gnomad FIN AF: 0.00405

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0177

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

GnomAD4 genome AF: 0.0257 AC: 3911 AN: 152312 Hom.: 114 Cov.: 32 AF XY: 0.0254 AC XY: 1893 AN XY: 74486

African (AFR) AF: 0.0655 AC: 2721 AN: 41554

American (AMR) AF: 0.0111 AC: 170 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0124 AC: 43 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0402 AC: 194 AN: 4828

European-Finnish (FIN) AF: 0.00405 AC: 43 AN: 10622

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0101 AC: 688 AN: 68028

Other (OTH) AF: 0.0175 AC: 37 AN: 2114

Alfa AF: 0.0178 Hom.: 18

Bravo AF: 0.0275

Asia WGS AF: 0.0170 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	10
DANN	Benign	0.44
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs72927357; hg19: chr4-101901410;