rs1636255

Positions:

• chr7-2853170-C-A
• chr7-2853170-C-T

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 0.236 in 152,032 control chromosomes in the GnomAD database, including 4,974 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 0.24 (4974 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35807 AN: 151914 Hom.: 4973 Cov.: 32

Gnomad AFR AF: 0.0931

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.236 AC: 35807 AN: 152032 Hom.: 4974 Cov.: 32 AF XY: 0.239 AC XY: 17756 AN XY: 74300

Gnomad4 AFR AF: 0.0929

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.245

Alfa AF: 0.246 Hom.: 2753

Bravo AF: 0.224

Asia WGS AF: 0.244 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.62
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1636255; hg19: chr7-2892804;