rs1578971

Variant names:

• chr11-9357458-C-T
• rs1578971

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 0.29 in 152,014 control chromosomes in the GnomAD database, including 7,396 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 0.29 (7396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 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: 0.290 AC: 44072 AN: 151896 Hom.: 7394 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.290 AC: 44090 AN: 152014 Hom.: 7396 Cov.: 32 AF XY: 0.289 AC XY: 21439 AN XY: 74286

African (AFR) AF: 0.132 AC: 5466 AN: 41498

American (AMR) AF: 0.327 AC: 4984 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1627 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1133 AN: 5180

South Asian (SAS) AF: 0.298 AC: 1436 AN: 4816

European-Finnish (FIN) AF: 0.356 AC: 3742 AN: 10516

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24631 AN: 67974

Other (OTH) AF: 0.344 AC: 725 AN: 2110

Alfa AF: 0.354 Hom.: 18258

Bravo AF: 0.284

Asia WGS AF: 0.283 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.5
DANN	Benign	0.81
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1578971; hg19: chr11-9379005;