6-70958144-C-T

Variant names:

• chr6-70958144-C-T
• rs10945275
• ENST00000718740.1:n.1592C>T

Variant summary

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

The ENST00000718740.1(ENSG00000293752):​n.1592C>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 0.234 in 152,058 control chromosomes in the GnomAD database, including 5,197 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 0.23 (5197 hom., cov: 32)
• Consequence: ENSG00000293752 ENST00000718740.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 3 publications found

Genes affected

ENSG00000293752 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901229	XM_047419611.1	c.*786C>T		3_prime_UTR_variant	Exon 2 of 2		XP_047275567.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293752	ENST00000718740.1	n.1592C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35523 AN: 151940 Hom.: 5190 Cov.: 32

Gnomad AFR AF: 0.0703

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.234 AC: 35536 AN: 152058 Hom.: 5197 Cov.: 32 AF XY: 0.239 AC XY: 17767 AN XY: 74320

African (AFR) AF: 0.0702 AC: 2914 AN: 41516

American (AMR) AF: 0.224 AC: 3425 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3468

East Asian (EAS) AF: 0.301 AC: 1552 AN: 5164

South Asian (SAS) AF: 0.405 AC: 1945 AN: 4806

European-Finnish (FIN) AF: 0.384 AC: 4059 AN: 10558

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20262 AN: 67938

Other (OTH) AF: 0.238 AC: 504 AN: 2114

Alfa AF: 0.249 Hom.: 1922

Bravo AF: 0.209

Asia WGS AF: 0.368 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.9
DANN	Benign	0.41
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs10945275; hg19: chr6-71667847;