1-164443610-G-T

Variant names:

• chr1-164443610-G-T
• rs1289726

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 0.113 in 152,066 control chromosomes in the GnomAD database, including 1,308 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 (1308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 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: 0.113 AC: 17161 AN: 151948 Hom.: 1306 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0703

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0907

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.113 AC: 17178 AN: 152066 Hom.: 1308 Cov.: 32 AF XY: 0.115 AC XY: 8564 AN XY: 74340

African (AFR) AF: 0.121 AC: 5002 AN: 41488

American (AMR) AF: 0.128 AC: 1950 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0375 AC: 130 AN: 3466

East Asian (EAS) AF: 0.432 AC: 2225 AN: 5156

South Asian (SAS) AF: 0.118 AC: 568 AN: 4824

European-Finnish (FIN) AF: 0.0703 AC: 744 AN: 10576

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0907 AC: 6161 AN: 67964

Other (OTH) AF: 0.109 AC: 230 AN: 2104

Alfa AF: 0.0922 Hom.: 1187

Bravo AF: 0.118

Asia WGS AF: 0.267 AC: 927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.48
DANN	Benign	0.72
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs1289726; hg19: chr1-164412847;