4-99408536-A-T

Variant names:

• chr4-99408536-A-T
• rs969804

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 0.462 in 151,898 control chromosomes in the GnomAD database, including 17,478 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 0.46 (17478 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 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: 0.462 AC: 70084 AN: 151780 Hom.: 17467 Cov.: 31

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.462 AC: 70140 AN: 151898 Hom.: 17478 Cov.: 31 AF XY: 0.460 AC XY: 34165 AN XY: 74232

African (AFR) AF: 0.655 AC: 27110 AN: 41414

American (AMR) AF: 0.354 AC: 5401 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1055 AN: 3468

East Asian (EAS) AF: 0.614 AC: 3166 AN: 5160

South Asian (SAS) AF: 0.502 AC: 2417 AN: 4816

European-Finnish (FIN) AF: 0.325 AC: 3426 AN: 10536

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26256 AN: 67936

Other (OTH) AF: 0.427 AC: 898 AN: 2104

Alfa AF: 0.248 Hom.: 534

Bravo AF: 0.472

Asia WGS AF: 0.470 AC: 1631 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.43
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs969804; hg19: chr4-100329693;