rs41460346

chr7-10329030-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 140 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0320

Gnomad4 AMR AF: 0.0356

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0120

Gnomad4 FIN AF: 0.0794

Gnomad4 NFE AF: 0.0453

Gnomad4 OTH AF: 0.0445

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41460346; hg19: chr7-10368657;