chr6-11920284-T-C

Variant names:

• chr6-11920284-T-C
• rs169713
• ENST00000848130.1:n.333+19112T>C

Variant summary

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

The ENST00000848130.1(ENSG00000310201):​n.333+19112T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,042 control chromosomes in the GnomAD database, including 9,289 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 0.31 (9289 hom., cov: 32)
• Consequence: ENSG00000310201 ENST00000848130.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 10 publications found

Genes affected

ENSG00000310201 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310201	ENST00000848130.1	n.333+19112T>C		intron_variant	Intron 1 of 2
ENSG00000310201	ENST00000848131.1	n.237+19112T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47083 AN: 151926 Hom.: 9256 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.310 AC: 47159 AN: 152042 Hom.: 9289 Cov.: 32 AF XY: 0.306 AC XY: 22769 AN XY: 74344

African (AFR) AF: 0.559 AC: 23151 AN: 41414

American (AMR) AF: 0.224 AC: 3431 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3468

East Asian (EAS) AF: 0.147 AC: 763 AN: 5178

South Asian (SAS) AF: 0.312 AC: 1502 AN: 4820

European-Finnish (FIN) AF: 0.199 AC: 2113 AN: 10592

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14563 AN: 67972

Other (OTH) AF: 0.338 AC: 713 AN: 2110

Alfa AF: 0.251 Hom.: 9337

Bravo AF: 0.320

Asia WGS AF: 0.253 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.67
DANN	Benign	0.39
PhyloP100		-0.034

Splicing

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

Other links and lift over

dbSNP: rs169713; hg19: chr6-11920517;