rs1662037

chr4-99357662-G-A

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 0.234 in 152,122 control chromosomes in the GnomAD database, including 4,941 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 0.23 (4941 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35604 AN: 152004 Hom.: 4938 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.0218

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.234 AC: 35617 AN: 152122 Hom.: 4941 Cov.: 32 AF XY: 0.232 AC XY: 17285 AN XY: 74366

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.0218

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.212

Alfa AF: 0.286 Hom.: 8153

Bravo AF: 0.214

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	11
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1662037; hg19: chr4-100278819;