chr12-77162822-G-T

Variant names:

• chr12-77162822-G-T
• rs1498744
• ENST00000667988.1:n.43-111G>T

Variant summary

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

The ENST00000667988.1(ENSG00000286476):​n.43-111G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0942 in 151,696 control chromosomes in the GnomAD database, including 1,612 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 0.094 (1612 hom., cov: 32)
• Consequence: ENSG00000286476 ENST00000667988.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 2 publications found

Genes affected

ENSG00000286476 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903107	XR_007063644.1	n.*104C>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286476	ENST00000667988.1	n.43-111G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0941 AC: 14264 AN: 151582 Hom.: 1608 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0496

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0131

Gnomad FIN AF: 0.0183

Gnomad MID AF: 0.0962

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.0797

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

GnomAD4 genome AF: 0.0942 AC: 14292 AN: 151696 Hom.: 1612 Cov.: 32 AF XY: 0.0903 AC XY: 6696 AN XY: 74154

African (AFR) AF: 0.270 AC: 11158 AN: 41352

American (AMR) AF: 0.0496 AC: 754 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3470

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5158

South Asian (SAS) AF: 0.0131 AC: 63 AN: 4816

European-Finnish (FIN) AF: 0.0183 AC: 192 AN: 10510

Middle Eastern (MID) AF: 0.0972 AC: 28 AN: 288

European-Non Finnish (NFE) AF: 0.0263 AC: 1784 AN: 67876

Other (OTH) AF: 0.0779 AC: 164 AN: 2104

Alfa AF: 0.0225 Hom.: 26

Bravo AF: 0.106

Asia WGS AF: 0.0250 AC: 86 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.53
DANN	Benign	0.63
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1498744; hg19: chr12-77556602;