rs41515

Variant names:

• chr7-104288515-A-C
• rs41515

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 0.589 in 152,056 control chromosomes in the GnomAD database, including 28,485 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 0.59 (28485 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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: 0.588 AC: 89407 AN: 151938 Hom.: 28448 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.589 AC: 89506 AN: 152056 Hom.: 28485 Cov.: 32 AF XY: 0.593 AC XY: 44078 AN XY: 74326

African (AFR) AF: 0.814 AC: 33774 AN: 41514

American (AMR) AF: 0.642 AC: 9805 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1528 AN: 3470

East Asian (EAS) AF: 0.873 AC: 4515 AN: 5172

South Asian (SAS) AF: 0.584 AC: 2817 AN: 4824

European-Finnish (FIN) AF: 0.475 AC: 5014 AN: 10560

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30224 AN: 67928

Other (OTH) AF: 0.586 AC: 1237 AN: 2110

Alfa AF: 0.486 Hom.: 9805

Bravo AF: 0.613

Asia WGS AF: 0.691 AC: 2402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.74
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs41515; hg19: chr7-103928963;