rs2227631

Variant names:

• chr7-101126257-A-G
• rs2227631

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 0.533 in 151,944 control chromosomes in the GnomAD database, including 23,184 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 0.53 (23184 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 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: 0.533 AC: 80938 AN: 151826 Hom.: 23123 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.533 AC: 81060 AN: 151944 Hom.: 23184 Cov.: 31 AF XY: 0.538 AC XY: 39943 AN XY: 74234

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.558

Alfa AF: 0.444 Hom.: 23861

Bravo AF: 0.555

Asia WGS AF: 0.607 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.7
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2227631; hg19: chr7-100769538;