chr1-150537646-C-T

Variant names:

• chr1-150537646-C-T
• rs11810419

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 0.138 in 152,164 control chromosomes in the GnomAD database, including 1,959 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 0.14 (1959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 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: 0.138 AC: 20917 AN: 152046 Hom.: 1953 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0289

Gnomad EAS AF: 0.0596

Gnomad SAS AF: 0.0506

Gnomad FIN AF: 0.0886

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0934

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.138 AC: 20940 AN: 152164 Hom.: 1959 Cov.: 32 AF XY: 0.134 AC XY: 10002 AN XY: 74400

African (AFR) AF: 0.256 AC: 10633 AN: 41502

American (AMR) AF: 0.135 AC: 2069 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0289 AC: 100 AN: 3466

East Asian (EAS) AF: 0.0593 AC: 307 AN: 5176

South Asian (SAS) AF: 0.0504 AC: 243 AN: 4822

European-Finnish (FIN) AF: 0.0886 AC: 939 AN: 10600

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0934 AC: 6351 AN: 67986

Other (OTH) AF: 0.111 AC: 235 AN: 2108

Alfa AF: 0.112 Hom.: 2374

Bravo AF: 0.149

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.43
DANN	Benign	0.23
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs11810419; hg19: chr1-150510122;