rs1465150

Variant names:

• chr6-119908361-C-T
• rs1465150

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 0.158 in 152,110 control chromosomes in the GnomAD database, including 2,060 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 0.16 (2060 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 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: 0.158 AC: 24061 AN: 151992 Hom.: 2060 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.158 AC: 24060 AN: 152110 Hom.: 2060 Cov.: 32 AF XY: 0.155 AC XY: 11539 AN XY: 74372

African (AFR) AF: 0.189 AC: 7845 AN: 41472

American (AMR) AF: 0.108 AC: 1646 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 574 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5178

South Asian (SAS) AF: 0.164 AC: 791 AN: 4818

European-Finnish (FIN) AF: 0.139 AC: 1471 AN: 10598

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11219 AN: 67986

Other (OTH) AF: 0.161 AC: 339 AN: 2110

Alfa AF: 0.160 Hom.: 353

Bravo AF: 0.157

Asia WGS AF: 0.0700 AC: 243 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.1
DANN	Benign	0.82
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1465150; hg19: chr6-120229507;