rs1627770

Variant names:

• chr12-33996498-G-T
• rs1627770

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 0.255 in 151,732 control chromosomes in the GnomAD database, including 5,534 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 0.26 (5534 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 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: 0.255 AC: 38670 AN: 151616 Hom.: 5524 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.255 AC: 38717 AN: 151732 Hom.: 5534 Cov.: 31 AF XY: 0.252 AC XY: 18681 AN XY: 74142

African (AFR) AF: 0.383 AC: 15852 AN: 41386

American (AMR) AF: 0.206 AC: 3138 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3472

East Asian (EAS) AF: 0.127 AC: 652 AN: 5150

South Asian (SAS) AF: 0.126 AC: 609 AN: 4818

European-Finnish (FIN) AF: 0.201 AC: 2109 AN: 10492

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.217 AC: 14754 AN: 67884

Other (OTH) AF: 0.231 AC: 488 AN: 2112

Alfa AF: 0.232 Hom.: 8332

Bravo AF: 0.262

Asia WGS AF: 0.154 AC: 534 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.28
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1627770; hg19: chr12-34149433;