rs625847

Variant names:

• chr1-12166660-G-A
• rs625847
• ENST00000782365.1:n.110+750C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000782365.1(ENSG00000301863):​n.110+750C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0383 in 152,334 control chromosomes in the GnomAD database, including 122 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 0.038 (122 hom., cov: 32)
• Consequence: ENSG00000301863 ENST00000782365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560
• Publications: 3 publications found

Genes affected

ENSG00000301863 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0383 (5829/152334) while in subpopulation AFR AF = 0.0456 (1896/41582). AF 95% confidence interval is 0.0439. There are 122 homozygotes in GnomAd4. There are 2647 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 122 gene

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
ENSG00000301863	ENST00000782365.1	n.110+750C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0381 AC: 5804 AN: 152216 Hom.: 117 Cov.: 32

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.0136

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0444

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0383 AC: 5829 AN: 152334 Hom.: 122 Cov.: 32 AF XY: 0.0355 AC XY: 2647 AN XY: 74494

African (AFR) AF: 0.0456 AC: 1896 AN: 41582

American (AMR) AF: 0.0203 AC: 310 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3472

East Asian (EAS) AF: 0.0137 AC: 71 AN: 5190

South Asian (SAS) AF: 0.0236 AC: 114 AN: 4828

European-Finnish (FIN) AF: 0.0165 AC: 175 AN: 10610

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0443 AC: 3017 AN: 68034

Other (OTH) AF: 0.0365 AC: 77 AN: 2112

Alfa AF: 0.0367 Hom.: 14

Bravo AF: 0.0382

Asia WGS AF: 0.0250 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.63
PhyloP100		-0.56
PromoterAI		-0.015	Neutral

Splicing

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

Other links and lift over

dbSNP: rs625847; hg19: chr1-12226717; COSMIC: COSV66163768;