rs917118

Variant names:

• chr7-4417372-C-T
• rs917118

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 0.383 in 151,858 control chromosomes in the GnomAD database, including 12,945 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 0.38 (12945 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 20 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 = 0.616 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: 0.382 AC: 58033 AN: 151740 Hom.: 12913 Cov.: 31

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.383 AC: 58118 AN: 151858 Hom.: 12945 Cov.: 31 AF XY: 0.385 AC XY: 28585 AN XY: 74186

African (AFR) AF: 0.622 AC: 25761 AN: 41406

American (AMR) AF: 0.357 AC: 5447 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3464

East Asian (EAS) AF: 0.297 AC: 1528 AN: 5142

South Asian (SAS) AF: 0.445 AC: 2135 AN: 4796

European-Finnish (FIN) AF: 0.270 AC: 2846 AN: 10530

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.271 AC: 18389 AN: 67948

Other (OTH) AF: 0.359 AC: 758 AN: 2112

Alfa AF: 0.309 Hom.: 35107

Bravo AF: 0.397

Asia WGS AF: 0.381 AC: 1325 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	1.6
DANN	Benign	0.19
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs917118; hg19: chr7-4457003;