rs975369

Variant names:

• chr7-25573041-G-A
• rs975369

Your query was ambiguous. Multiple possible variants found:

• chr7-25573041-G-A
• chr7-25573041-G-T

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 0.0941 in 152,240 control chromosomes in the GnomAD database, including 1,015 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 (1015 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.494

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 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: 0.0940 AC: 14307 AN: 152124 Hom.: 1016 Cov.: 32

Gnomad AFR AF: 0.0851

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0996

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0667

Gnomad OTH AF: 0.0894

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

GnomAD4 genome AF: 0.0941 AC: 14326 AN: 152240 Hom.: 1015 Cov.: 32 AF XY: 0.0995 AC XY: 7404 AN XY: 74430

Gnomad4 AFR AF: 0.0854

Gnomad4 AMR AF: 0.0997

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.0876

Gnomad4 NFE AF: 0.0667

Gnomad4 OTH AF: 0.0918

Alfa AF: 0.0699 Hom.: 435

Bravo AF: 0.0957

Asia WGS AF: 0.261 AC: 905 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs975369; hg19: chr7-25612661;