rs13222905

Variant names:

• chr7-150566901-G-A
• rs13222905

Your query was ambiguous. Multiple possible variants found:

• chr7-150566901-G-A
• chr7-150566901-G-C

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 0.145 in 152,098 control chromosomes in the GnomAD database, including 1,669 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 0.15 (1669 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 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: 0.145 AC: 22086 AN: 151980 Hom.: 1673 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.145 AC: 22090 AN: 152098 Hom.: 1669 Cov.: 31 AF XY: 0.145 AC XY: 10767 AN XY: 74324

African (AFR) AF: 0.120 AC: 4978 AN: 41488

American (AMR) AF: 0.133 AC: 2034 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0850 AC: 295 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1051 AN: 5154

South Asian (SAS) AF: 0.119 AC: 574 AN: 4820

European-Finnish (FIN) AF: 0.188 AC: 1994 AN: 10584

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10625 AN: 67972

Other (OTH) AF: 0.159 AC: 337 AN: 2114

Alfa AF: 0.116 Hom.: 296

Bravo AF: 0.140

Asia WGS AF: 0.176 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.1
DANN	Benign	0.76
PhyloP100		0.35
PromoterAI		-0.0096	Neutral

Splicing

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

Other links and lift over

dbSNP: rs13222905; hg19: chr7-150263989;