rs2227631

chr7-101126257-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;