chr11-61492279-T-C

Variant names:

• chr11-61492279-T-C
• rs7947046

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 0.128 in 150,796 control chromosomes in the GnomAD database, including 1,513 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 0.13 (1513 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.22
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 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: 0.127 AC: 19144 AN: 150678 Hom.: 1486 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0914

Gnomad OTH AF: 0.0938

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

GnomAD4 genome AF: 0.128 AC: 19234 AN: 150796 Hom.: 1513 Cov.: 32 AF XY: 0.129 AC XY: 9487 AN XY: 73594

African (AFR) AF: 0.216 AC: 8828 AN: 40964

American (AMR) AF: 0.114 AC: 1727 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 179 AN: 3450

East Asian (EAS) AF: 0.0133 AC: 68 AN: 5120

South Asian (SAS) AF: 0.162 AC: 772 AN: 4762

European-Finnish (FIN) AF: 0.118 AC: 1216 AN: 10308

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.0914 AC: 6185 AN: 67706

Other (OTH) AF: 0.0995 AC: 209 AN: 2100

Alfa AF: 0.0949 Hom.: 968

Bravo AF: 0.130

Asia WGS AF: 0.117 AC: 407 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	0.18
DANN	Benign	0.36
PhyloP100		-6.2

Splicing

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

Other links and lift over

dbSNP: rs7947046; hg19: chr11-61259751;