1-147774791-T-G

Variant names:

• chr1-147774791-T-G
• rs12408178
• ENST00000721952.1:n.386+5876A>C

Variant summary

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

The ENST00000721952.1(ENSG00000294222):​n.386+5876A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,236 control chromosomes in the GnomAD database, including 3,268 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 0.19 (3268 hom., cov: 33)
• Consequence: ENSG00000294222 ENST00000721952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.718
• Publications: 9 publications found

Genes affected

ENSG00000294222 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723321	XR_922079.4	n.82-2770T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294222	ENST00000721952.1	n.386+5876A>C		intron_variant	Intron 1 of 2
ENSG00000294222	ENST00000721953.1	n.388+5876A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29476 AN: 152118 Hom.: 3269 Cov.: 33

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.194 AC: 29486 AN: 152236 Hom.: 3268 Cov.: 33 AF XY: 0.193 AC XY: 14400 AN XY: 74434

African (AFR) AF: 0.0773 AC: 3210 AN: 41550

American (AMR) AF: 0.251 AC: 3844 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3468

East Asian (EAS) AF: 0.322 AC: 1670 AN: 5180

South Asian (SAS) AF: 0.176 AC: 852 AN: 4830

European-Finnish (FIN) AF: 0.230 AC: 2438 AN: 10598

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16062 AN: 68000

Other (OTH) AF: 0.212 AC: 448 AN: 2112

Alfa AF: 0.221 Hom.: 3197

Bravo AF: 0.194

Asia WGS AF: 0.242 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs12408178; hg19: chr1-147246903;