1-17307077-G-T

Variant names:

• chr1-17307077-G-T
• rs2477134

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 0.635 in 152,096 control chromosomes in the GnomAD database, including 30,888 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 0.63 (30888 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 12 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 = 0.843 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: 0.635 AC: 96508 AN: 151978 Hom.: 30865 Cov.: 34

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.635 AC: 96577 AN: 152096 Hom.: 30888 Cov.: 34 AF XY: 0.635 AC XY: 47224 AN XY: 74338

African (AFR) AF: 0.575 AC: 23834 AN: 41480

American (AMR) AF: 0.641 AC: 9806 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2440 AN: 3468

East Asian (EAS) AF: 0.864 AC: 4462 AN: 5166

South Asian (SAS) AF: 0.644 AC: 3107 AN: 4828

European-Finnish (FIN) AF: 0.626 AC: 6618 AN: 10574

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44267 AN: 67970

Other (OTH) AF: 0.635 AC: 1340 AN: 2110

Alfa AF: 0.565 Hom.: 2985

Bravo AF: 0.638

Asia WGS AF: 0.743 AC: 2581 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	2.1
DANN	Benign	0.69
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs2477134; hg19: chr1-17633572;