rs41460346

Variant names:

• chr7-10329030-G-A
• rs41460346

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0399 in 152,034 control chromosomes in the GnomAD database, including 144 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 0.040 (144 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0399 (6073/152034) while in subpopulation NFE AF = 0.0453 (3079/67952). AF 95% confidence interval is 0.044. There are 144 homozygotes in GnomAd4. There are 3009 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 144 gene

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: 0.0399 AC: 6065 AN: 151916 Hom.: 140 Cov.: 32

Gnomad AFR AF: 0.0320

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0357

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0120

Gnomad FIN AF: 0.0794

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0453

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0399 AC: 6073 AN: 152034 Hom.: 144 Cov.: 32 AF XY: 0.0405 AC XY: 3009 AN XY: 74320

African (AFR) AF: 0.0320 AC: 1326 AN: 41490

American (AMR) AF: 0.0356 AC: 543 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5178

South Asian (SAS) AF: 0.0120 AC: 58 AN: 4822

European-Finnish (FIN) AF: 0.0794 AC: 838 AN: 10552

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0453 AC: 3079 AN: 67952

Other (OTH) AF: 0.0445 AC: 94 AN: 2112

Alfa AF: 0.0404 Hom.: 17

Bravo AF: 0.0378

Asia WGS AF: 0.0280 AC: 97 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0010
DANN	Benign	0.46
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs41460346; hg19: chr7-10368657;