7-1173491-A-G

Variant names:

• chr7-1173491-A-G
• rs1543985

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 0.696 in 152,166 control chromosomes in the GnomAD database, including 38,039 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 0.70 (38039 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 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: 0.696 AC: 105806 AN: 152048 Hom.: 37988 Cov.: 33

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.696 AC: 105908 AN: 152166 Hom.: 38039 Cov.: 33 AF XY: 0.692 AC XY: 51476 AN XY: 74386

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.657

Alfa AF: 0.640 Hom.: 27558

Bravo AF: 0.700

Asia WGS AF: 0.560 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1543985; hg19: chr7-1213127;