rs7928165

Variant names:

• chr11-42773547-A-C
• rs7928165

Your query was ambiguous. Multiple possible variants found:

• chr11-42773547-A-C
• chr11-42773547-A-G

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 0.374 in 152,060 control chromosomes in the GnomAD database, including 10,737 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 0.37 (10737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.386 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: 0.374 AC: 56795 AN: 151942 Hom.: 10730 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.374 AC: 56831 AN: 152060 Hom.: 10737 Cov.: 32 AF XY: 0.377 AC XY: 28005 AN XY: 74314

African (AFR) AF: 0.382 AC: 15860 AN: 41476

American (AMR) AF: 0.324 AC: 4943 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1481 AN: 3466

East Asian (EAS) AF: 0.234 AC: 1209 AN: 5162

South Asian (SAS) AF: 0.401 AC: 1933 AN: 4826

European-Finnish (FIN) AF: 0.460 AC: 4862 AN: 10566

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.372 AC: 25280 AN: 67972

Other (OTH) AF: 0.361 AC: 761 AN: 2110

Alfa AF: 0.366 Hom.: 30382

Bravo AF: 0.361

Asia WGS AF: 0.298 AC: 1039 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	2.7
DANN	Benign	0.44
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs7928165; hg19: chr11-42795097;