rs7447447

Variant names:

• chr5-105532235-C-T
• rs7447447

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 0.106 in 152,258 control chromosomes in the GnomAD database, including 1,098 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 0.11 (1098 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.28 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: 0.106 AC: 16080 AN: 152140 Hom.: 1098 Cov.: 32

Gnomad AFR AF: 0.0317

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.106 AC: 16080 AN: 152258 Hom.: 1098 Cov.: 32 AF XY: 0.109 AC XY: 8123 AN XY: 74440

African (AFR) AF: 0.0317 AC: 1317 AN: 41568

American (AMR) AF: 0.119 AC: 1817 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3470

East Asian (EAS) AF: 0.180 AC: 933 AN: 5184

South Asian (SAS) AF: 0.292 AC: 1411 AN: 4826

European-Finnish (FIN) AF: 0.136 AC: 1442 AN: 10592

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8346 AN: 68016

Other (OTH) AF: 0.111 AC: 234 AN: 2114

Alfa AF: 0.0940 Hom.: 413

Bravo AF: 0.0972

Asia WGS AF: 0.222 AC: 773 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	1.0
DANN	Benign	0.48
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs7447447; hg19: chr5-104867936;