rs935181

Variant names:

• chr6-160927037-T-C
• rs935181
• ENST00000420601.1:n.254T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000420601.1(ENSG00000231863):​n.254T>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: ENSG00000231863 ENST00000420601.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 6 publications found

Genes affected

ENSG00000231863 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC102724087	NR_187755.1	n.138T>C		non_coding_transcript_exon_variant	Exon 2 of 6
LOC102724087	NR_187758.1	n.144T>C		non_coding_transcript_exon_variant	Exon 2 of 6
LOC102724087	NR_187759.1	n.144T>C		non_coding_transcript_exon_variant	Exon 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231863	ENST00000420601.1	n.254T>C		non_coding_transcript_exon_variant	Exon 2 of 2	2
ENSG00000231863	ENST00000653049.1	n.88T>C		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000231863	ENST00000663228.1	n.81T>C		non_coding_transcript_exon_variant	Exon 2 of 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

African (AFR) AF: 0.500 AC: 1 AN: 2

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) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.227 AC: 5 AN: 22

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.371 AC: 15374 AN: 41408

American (AMR) AF: 0.193 AC: 2947 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1208 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5174

South Asian (SAS) AF: 0.128 AC: 616 AN: 4816

European-Finnish (FIN) AF: 0.202 AC: 2138 AN: 10586

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16704 AN: 67960

Other (OTH) AF: 0.249 AC: 525 AN: 2108

Alfa AF: 0.252 Hom.: 15159

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs935181; hg19: chr6-161348069;