rs935181

Positions:

• chr6-160927037-T-C
• chr6-160927037-T-G

Variant summary

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

The ENST00000663228.1(ENSG00000233342):​n.81T>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 0.261 in 152,044 control chromosomes in the GnomAD database, including 5,708 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 0.26 (5707 hom., cov: 31)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: ENST00000663228.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724087	XR_007059855.1	n.149-69T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663228.1	n.81T>C		non_coding_transcript_exon_variant	2/4
	ENST00000420601.1	n.254T>C		non_coding_transcript_exon_variant	2/2	2
	ENST00000653049.1	n.88T>C		non_coding_transcript_exon_variant	2/4

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39680 AN: 151898 Hom.: 5707 Cov.: 31

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.252

GnomAD4 exome AF: 0.250 AC: 7 AN: 28 Hom.: 1 Cov.: 0 AF XY: 0.318 AC XY: 7 AN XY: 22

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.227

GnomAD4 genome AF: 0.261 AC: 39704 AN: 152016 Hom.: 5707 Cov.: 31 AF XY: 0.256 AC XY: 19034 AN XY: 74310

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.249

Alfa AF: 0.246 Hom.: 9566

Bravo AF: 0.269

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.70
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs935181; hg19: chr6-161348069;