chr6-88172933-T-C

Variant names:

• chr6-88172933-T-C
• rs10485170
• ENST00000624253.1:n.673T>C

Variant summary

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

The ENST00000624253.1(ENSG00000279565):​n.673T>C 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 0.141 in 152,220 control chromosomes in the GnomAD database, including 2,011 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 0.14 (2011 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000279565 ENST00000624253.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 19 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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624253.1. 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
	ENSG00000279565	ENST00000624253.1	TSL:6	n.673T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298549	ENST00000756364.1		n.129-38664T>C		intron	N/A
	ENSG00000298549	ENST00000756365.1		n.571+2664T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21468 AN: 152102 Hom.: 2009 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0923

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0808

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.121

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

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) AF: 0.00 AC: 0 AN: 2

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

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.141 AC: 21485 AN: 152220 Hom.: 2011 Cov.: 32 AF XY: 0.138 AC XY: 10311 AN XY: 74452

African (AFR) AF: 0.268 AC: 11113 AN: 41492

American (AMR) AF: 0.0921 AC: 1409 AN: 15298

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

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5188

South Asian (SAS) AF: 0.0800 AC: 386 AN: 4822

European-Finnish (FIN) AF: 0.104 AC: 1105 AN: 10618

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0990 AC: 6735 AN: 68010

Other (OTH) AF: 0.120 AC: 253 AN: 2116

Alfa AF: 0.112 Hom.: 3659

Bravo AF: 0.146

Asia WGS AF: 0.0650 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.4
DANN	Benign	0.63
PhyloP100		0.20

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: rs10485170;

hg19: chr6-88882652;