4-99366692-C-T

Variant names:

• chr4-99366692-C-T
• rs1154442

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 0.314 in 152,044 control chromosomes in the GnomAD database, including 8,935 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 0.31 (8935 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 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: 0.314 AC: 47744 AN: 151928 Hom.: 8928 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.314 AC: 47767 AN: 152044 Hom.: 8935 Cov.: 32 AF XY: 0.315 AC XY: 23409 AN XY: 74332

African (AFR) AF: 0.144 AC: 5985 AN: 41472

American (AMR) AF: 0.294 AC: 4485 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3472

East Asian (EAS) AF: 0.0820 AC: 423 AN: 5158

South Asian (SAS) AF: 0.308 AC: 1481 AN: 4814

European-Finnish (FIN) AF: 0.515 AC: 5445 AN: 10576

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28069 AN: 67956

Other (OTH) AF: 0.288 AC: 608 AN: 2114

Alfa AF: 0.257 Hom.: 795

Bravo AF: 0.288

Asia WGS AF: 0.220 AC: 761 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.35
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1154442; hg19: chr4-100287849; COSMIC: COSV107199795;