4-66435324-A-T

Variant names:

• chr4-66435324-A-T
• rs1949200

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 0.182 in 152,028 control chromosomes in the GnomAD database, including 2,734 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 0.18 (2734 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 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: 0.182 AC: 27662 AN: 151910 Hom.: 2732 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.182 AC: 27685 AN: 152028 Hom.: 2734 Cov.: 32 AF XY: 0.185 AC XY: 13769 AN XY: 74290

African (AFR) AF: 0.238 AC: 9873 AN: 41460

American (AMR) AF: 0.224 AC: 3426 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3472

East Asian (EAS) AF: 0.268 AC: 1383 AN: 5162

South Asian (SAS) AF: 0.223 AC: 1073 AN: 4814

European-Finnish (FIN) AF: 0.159 AC: 1682 AN: 10576

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9238 AN: 67968

Other (OTH) AF: 0.162 AC: 341 AN: 2108

Alfa AF: 0.0754 Hom.: 91

Bravo AF: 0.187

Asia WGS AF: 0.217 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.31
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1949200; hg19: chr4-67301042;