rs4236601

Variant names:

• chr7-116522675-G-A
• rs4236601

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 0.274 in 152,128 control chromosomes in the GnomAD database, including 6,358 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 0.27 (6358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 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: 0.274 AC: 41718 AN: 152010 Hom.: 6356 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.274 AC: 41744 AN: 152128 Hom.: 6358 Cov.: 32 AF XY: 0.264 AC XY: 19658 AN XY: 74380

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.291

Alfa AF: 0.270 Hom.: 8547

Bravo AF: 0.287

Asia WGS AF: 0.0990 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4236601; hg19: chr7-116162729;