ENST00000624253.1:n.2842C>T

Variant names:

• chr6-88175102-C-T
• rs1406977
• ENST00000624253.1:n.2842C>T

Variant summary

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

The ENST00000624253.1(ENSG00000279565):​n.2842C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,196 control chromosomes in the GnomAD database, including 48,618 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 0.80 (48562 hom., cov: 30)
  • Exomes 𝑓: 0.75 (56 hom.)
• Consequence: ENSG00000279565 ENST00000624253.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 18 publications found

Genes affected

ENSG00000279565 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279565	ENST00000624253.1	n.2842C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000298549	ENST00000756364.1	n.129-36495C>T		intron_variant	Intron 1 of 2
ENSG00000298549	ENST00000756365.1	n.571+4833C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121164 AN: 151880 Hom.: 48520 Cov.: 30

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.795

GnomAD4 exome AF: 0.747 AC: 148 AN: 198 Hom.: 56 Cov.: 0 AF XY: 0.771 AC XY: 108 AN XY: 140

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AF: 0.667 AC: 4 AN: 6

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 4 AN: 4

East Asian (EAS) AF: 0.667 AC: 4 AN: 6

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 4 AN: 8

Middle Eastern (MID) AF: 0.500 AC: 2 AN: 4

European-Non Finnish (NFE) AF: 0.763 AC: 119 AN: 156

Other (OTH) AF: 0.750 AC: 6 AN: 8

GnomAD4 genome AF: 0.798 AC: 121261 AN: 151998 Hom.: 48562 Cov.: 30 AF XY: 0.795 AC XY: 59078 AN XY: 74296

African (AFR) AF: 0.876 AC: 36308 AN: 41462

American (AMR) AF: 0.705 AC: 10766 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2542 AN: 3470

East Asian (EAS) AF: 0.778 AC: 4025 AN: 5172

South Asian (SAS) AF: 0.718 AC: 3459 AN: 4818

European-Finnish (FIN) AF: 0.747 AC: 7851 AN: 10514

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53691 AN: 67968

Other (OTH) AF: 0.792 AC: 1671 AN: 2110

Alfa AF: 0.784 Hom.: 77780

Bravo AF: 0.798

Asia WGS AF: 0.730 AC: 2542 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	1.3
DANN	Benign	0.48
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1406977; hg19: chr6-88884821;