12-77162822-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667988.1. 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
	ENSG00000286476	ENST00000667988.1		n.43-111G>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1498744;

hg19: chr12-77556602;