chr7-57346458-G-A

Variant names:

• chr7-57346458-G-A
• rs12538910

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 0.478 in 151,836 control chromosomes in the GnomAD database, including 18,203 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 0.48 (18203 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.712 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: 0.478 AC: 72473 AN: 151718 Hom.: 18167 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.478 AC: 72563 AN: 151836 Hom.: 18203 Cov.: 31 AF XY: 0.485 AC XY: 35974 AN XY: 74182

African (AFR) AF: 0.576 AC: 23861 AN: 41408

American (AMR) AF: 0.512 AC: 7809 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1209 AN: 3466

East Asian (EAS) AF: 0.732 AC: 3749 AN: 5124

South Asian (SAS) AF: 0.627 AC: 3017 AN: 4812

European-Finnish (FIN) AF: 0.478 AC: 5031 AN: 10526

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26589 AN: 67932

Other (OTH) AF: 0.447 AC: 944 AN: 2110

Alfa AF: 0.423 Hom.: 51908

Bravo AF: 0.484

Asia WGS AF: 0.672 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.45
DANN	Benign	0.53
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs12538910; hg19: chr7-57414165;