rs1072056

Variant names:

• chr5-111168417-C-A
• rs1072056

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 0.286 in 151,958 control chromosomes in the GnomAD database, including 6,422 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 (6422 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.358 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: 0.286 AC: 43419 AN: 151838 Hom.: 6421 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.286 AC: 43436 AN: 151958 Hom.: 6422 Cov.: 32 AF XY: 0.286 AC XY: 21249 AN XY: 74258

African (AFR) AF: 0.362 AC: 15021 AN: 41438

American (AMR) AF: 0.279 AC: 4262 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 786 AN: 3472

East Asian (EAS) AF: 0.200 AC: 1030 AN: 5146

South Asian (SAS) AF: 0.342 AC: 1651 AN: 4834

European-Finnish (FIN) AF: 0.236 AC: 2486 AN: 10546

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17395 AN: 67940

Other (OTH) AF: 0.269 AC: 566 AN: 2108

Alfa AF: 0.265 Hom.: 3270

Bravo AF: 0.289

Asia WGS AF: 0.286 AC: 994 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	2.1
DANN	Benign	0.61
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs1072056; hg19: chr5-110504115;