12-7642178-T-G

Position:

• chr12-7642178-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642279.1(ENSG00000285142):​n.373-4441A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 152,040 control chromosomes in the GnomAD database, including 26,969 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 0.56 (26969 hom., cov: 32)
• Consequence: ENST00000642279.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000642279.1	n.373-4441A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85763 AN: 151922 Hom.: 26978 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.564 AC: 85769 AN: 152040 Hom.: 26969 Cov.: 32 AF XY: 0.561 AC XY: 41673 AN XY: 74328

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.612

Alfa AF: 0.628 Hom.: 3991

Bravo AF: 0.539

Asia WGS AF: 0.490 AC: 1706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41384747; hg19: chr12-7794774;