rs2270628

Variant names:

• chr7-45909971-C-T
• rs2270628

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 0.24 in 152,134 control chromosomes in the GnomAD database, including 4,884 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 (4884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 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: 0.240 AC: 36417 AN: 152016 Hom.: 4864 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.0945

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.240 AC: 36478 AN: 152134 Hom.: 4884 Cov.: 32 AF XY: 0.236 AC XY: 17523 AN XY: 74362

African (AFR) AF: 0.367 AC: 15219 AN: 41496

American (AMR) AF: 0.165 AC: 2520 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 791 AN: 3470

East Asian (EAS) AF: 0.183 AC: 950 AN: 5182

South Asian (SAS) AF: 0.0940 AC: 453 AN: 4820

European-Finnish (FIN) AF: 0.234 AC: 2473 AN: 10574

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13514 AN: 67986

Other (OTH) AF: 0.216 AC: 455 AN: 2110

Alfa AF: 0.213 Hom.: 11168

Bravo AF: 0.245

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.44
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs2270628; hg19: chr7-45949570;