chr6-88173605-C-T

Variant names:

• chr6-88173605-C-T
• rs9450906
• ENST00000624253.1:n.1345C>T

Variant summary

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

The ENST00000624253.1(ENSG00000279565):​n.1345C>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 0.181 in 152,092 control chromosomes in the GnomAD database, including 3,956 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 0.18 (3956 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000279565 ENST00000624253.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 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.1345C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000298549	ENST00000756364.1	n.129-37992C>T		intron_variant	Intron 1 of 2
ENSG00000298549	ENST00000756365.1	n.571+3336C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27479 AN: 151974 Hom.: 3942 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.0800

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.149

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.181 AC: 27523 AN: 152092 Hom.: 3956 Cov.: 32 AF XY: 0.176 AC XY: 13114 AN XY: 74352

African (AFR) AF: 0.405 AC: 16784 AN: 41444

American (AMR) AF: 0.111 AC: 1694 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3470

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5176

South Asian (SAS) AF: 0.0790 AC: 380 AN: 4808

European-Finnish (FIN) AF: 0.104 AC: 1101 AN: 10572

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0995 AC: 6767 AN: 68004

Other (OTH) AF: 0.147 AC: 311 AN: 2114

Alfa AF: 0.153 Hom.: 372

Bravo AF: 0.190

Asia WGS AF: 0.0740 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.79
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs9450906; hg19: chr6-88883324;