1-152617711-C-T

Variant names:

• chr1-152617711-C-T
• rs6677595

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 0.58 in 151,638 control chromosomes in the GnomAD database, including 26,182 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 0.58 (26182 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 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: 0.580 AC: 87851 AN: 151520 Hom.: 26175 Cov.: 30

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.580 AC: 87892 AN: 151638 Hom.: 26182 Cov.: 30 AF XY: 0.584 AC XY: 43289 AN XY: 74088

African (AFR) AF: 0.422 AC: 17419 AN: 41284

American (AMR) AF: 0.622 AC: 9487 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2159 AN: 3470

East Asian (EAS) AF: 0.615 AC: 3148 AN: 5122

South Asian (SAS) AF: 0.631 AC: 3028 AN: 4800

European-Finnish (FIN) AF: 0.663 AC: 6962 AN: 10508

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.645 AC: 43770 AN: 67910

Other (OTH) AF: 0.581 AC: 1217 AN: 2096

Alfa AF: 0.617 Hom.: 111586

Bravo AF: 0.567

Asia WGS AF: 0.582 AC: 2024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs6677595; hg19: chr1-152590187;