rs4461115

Variant names:

• chr17-47722212-T-C
• rs4461115

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 0.193 in 152,208 control chromosomes in the GnomAD database, including 3,557 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 0.19 (3557 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 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: 0.193 AC: 29363 AN: 152088 Hom.: 3558 Cov.: 32

Gnomad AFR AF: 0.0595

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.193 AC: 29361 AN: 152208 Hom.: 3557 Cov.: 32 AF XY: 0.194 AC XY: 14427 AN XY: 74416

African (AFR) AF: 0.0594 AC: 2467 AN: 41556

American (AMR) AF: 0.159 AC: 2423 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 772 AN: 3468

East Asian (EAS) AF: 0.180 AC: 934 AN: 5184

South Asian (SAS) AF: 0.299 AC: 1440 AN: 4824

European-Finnish (FIN) AF: 0.256 AC: 2712 AN: 10584

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17911 AN: 67988

Other (OTH) AF: 0.192 AC: 405 AN: 2112

Alfa AF: 0.202 Hom.: 2955

Bravo AF: 0.176

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.61
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs4461115; hg19: chr17-45799578; COSMIC: COSV65116250;