1-231016391-T-C

Variant names:

• chr1-231016391-T-C
• rs7545429

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 0.482 in 151,730 control chromosomes in the GnomAD database, including 18,370 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 0.48 (18370 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.676 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: 0.482 AC: 73141 AN: 151614 Hom.: 18364 Cov.: 30

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.482 AC: 73194 AN: 151730 Hom.: 18370 Cov.: 30 AF XY: 0.485 AC XY: 35969 AN XY: 74180

African (AFR) AF: 0.597 AC: 24664 AN: 41322

American (AMR) AF: 0.418 AC: 6364 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1690 AN: 3466

East Asian (EAS) AF: 0.647 AC: 3330 AN: 5148

South Asian (SAS) AF: 0.695 AC: 3346 AN: 4812

European-Finnish (FIN) AF: 0.350 AC: 3679 AN: 10514

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28269 AN: 67922

Other (OTH) AF: 0.485 AC: 1021 AN: 2106

Alfa AF: 0.447 Hom.: 8798

Bravo AF: 0.487

Asia WGS AF: 0.620 AC: 2157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.77
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs7545429; hg19: chr1-231152137;