ENST00000824747.1:n.109+974A>C

Variant names:

• chr1-68466239-A-C
• rs12744671
• ENST00000824747.1:n.109+974A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000824747.1(ENSG00000307251):​n.109+974A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 152,212 control chromosomes in the GnomAD database, including 444 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 0.066 (444 hom., cov: 32)
• Consequence: ENSG00000307251 ENST00000824747.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 1 publications found

Genes affected

ENSG00000307251 (HGNC:):

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 = 0.0996 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824747.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307251	ENST00000824747.1		n.109+974A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0659 AC: 10022 AN: 152094 Hom.: 445 Cov.: 32

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0613

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0658 AC: 10017 AN: 152212 Hom.: 444 Cov.: 32 AF XY: 0.0632 AC XY: 4706 AN XY: 74436

African (AFR) AF: 0.0160 AC: 664 AN: 41542

American (AMR) AF: 0.0665 AC: 1016 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0253 AC: 122 AN: 4816

European-Finnish (FIN) AF: 0.0613 AC: 650 AN: 10608

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6908 AN: 68000

Other (OTH) AF: 0.0643 AC: 136 AN: 2114

Alfa AF: 0.0772 Hom.: 578

Bravo AF: 0.0645

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.36
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs12744671; hg19: chr1-68931922;