rs7548917

chr1-100773820-T-Cchr1-100773820-T-G

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 0.491 in 151,384 control chromosomes in the GnomAD database, including 18,659 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 0.49 (18659 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74262 AN: 151268 Hom.: 18646 Cov.: 29

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.491 AC: 74315 AN: 151384 Hom.: 18659 Cov.: 29 AF XY: 0.494 AC XY: 36509 AN XY: 73924

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.481

Alfa AF: 0.479 Hom.: 2945

Bravo AF: 0.497

Asia WGS AF: 0.552 AC: 1922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.72
Dann	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7548917; hg19: chr1-101239376; COSMIC: COSV59978413;