rs174627

Variant names:

• chr11-61869994-G-A
• rs174627

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 0.0997 in 152,302 control chromosomes in the GnomAD database, including 960 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 0.10 (960 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 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: 0.0998 AC: 15191 AN: 152186 Hom.: 962 Cov.: 33

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0848

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0956

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0997 AC: 15181 AN: 152302 Hom.: 960 Cov.: 33 AF XY: 0.0953 AC XY: 7096 AN XY: 74468

African (AFR) AF: 0.0436 AC: 1812 AN: 41574

American (AMR) AF: 0.0845 AC: 1292 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5190

South Asian (SAS) AF: 0.0468 AC: 226 AN: 4828

European-Finnish (FIN) AF: 0.0956 AC: 1014 AN: 10604

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9992 AN: 68020

Other (OTH) AF: 0.109 AC: 230 AN: 2112

Alfa AF: 0.126 Hom.: 714

Bravo AF: 0.0970

Asia WGS AF: 0.0270 AC: 93 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	0.61
DANN	Benign	0.71
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs174627; hg19: chr11-61637466;