rs946138

Variant names:

• chr6-78235177-G-A
• rs946138
• ENST00000715178.1:n.1038-31224C>T

Variant summary

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

The ENST00000715178.1(ENSG00000230309):​n.1038-31224C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,152 control chromosomes in the GnomAD database, including 1,024 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 0.11 (1024 hom., cov: 32)
• Consequence: ENSG00000230309 ENST00000715178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 4 publications found

Genes affected

ENSG00000230309 (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 (EAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377865	XR_002956359.2	n.135-31224C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230309	ENST00000715178.1	n.1038-31224C>T		intron_variant	Intron 6 of 14

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17255 AN: 152034 Hom.: 1024 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0876

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0626

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.113 AC: 17243 AN: 152152 Hom.: 1024 Cov.: 32 AF XY: 0.111 AC XY: 8231 AN XY: 74370

African (AFR) AF: 0.112 AC: 4653 AN: 41536

American (AMR) AF: 0.0875 AC: 1337 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3470

East Asian (EAS) AF: 0.149 AC: 771 AN: 5158

South Asian (SAS) AF: 0.105 AC: 507 AN: 4822

European-Finnish (FIN) AF: 0.0626 AC: 663 AN: 10584

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8216 AN: 67980

Other (OTH) AF: 0.115 AC: 244 AN: 2114

Alfa AF: 0.116 Hom.: 215

Bravo AF: 0.115

Asia WGS AF: 0.146 AC: 506 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	3.8
DANN	Benign	0.38
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs946138; hg19: chr6-78944894;