chr7-42286026-G-T

Variant names:

• chr7-42286026-G-T
• rs12532960

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B.

Score: -12 - Benign

-12

BP4_StrongBA1

The variant allele was found at a frequency of 0.0937 in 152,150 control chromosomes in the GnomAD database, including 798 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 0.094 (798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.603
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.132 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: 0.0938 AC: 14265 AN: 152032 Hom.: 799 Cov.: 32

Gnomad AFR AF: 0.0332

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.0287

Gnomad SAS AF: 0.0490

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0937 AC: 14261 AN: 152150 Hom.: 798 Cov.: 32 AF XY: 0.0931 AC XY: 6924 AN XY: 74374

African (AFR) AF: 0.0332 AC: 1377 AN: 41528

American (AMR) AF: 0.137 AC: 2088 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3470

East Asian (EAS) AF: 0.0288 AC: 149 AN: 5176

South Asian (SAS) AF: 0.0480 AC: 231 AN: 4814

European-Finnish (FIN) AF: 0.121 AC: 1275 AN: 10574

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8577 AN: 67982

Other (OTH) AF: 0.104 AC: 219 AN: 2114

Alfa AF: 0.114 Hom.: 2924

Bravo AF: 0.0925

Asia WGS AF: 0.0490 AC: 168 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.46
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs12532960; hg19: chr7-42325625;