chr6-157347549-T-C

Variant names:

• chr6-157347549-T-C
• rs4128492
• ENST00000796634.1:n.110-14188T>C

Variant summary

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

The ENST00000796634.1(ENSG00000303704):​n.110-14188T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,098 control chromosomes in the GnomAD database, including 5,651 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 0.27 (5651 hom., cov: 32)
• Consequence: ENSG00000303704 ENST00000796634.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 3 publications found

Genes affected

ENSG00000303704 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 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
ENSG00000303704	ENST00000796634.1	n.110-14188T>C		intron_variant	Intron 1 of 2
ENSG00000303704	ENST00000796635.1	n.246-14188T>C		intron_variant	Intron 2 of 3
ENSG00000303704	ENST00000796636.1	n.266-14188T>C		intron_variant	Intron 2 of 3
ENSG00000303704	ENST00000796637.1	n.393-14188T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40355 AN: 151980 Hom.: 5641 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.266 AC: 40401 AN: 152098 Hom.: 5651 Cov.: 32 AF XY: 0.269 AC XY: 19997 AN XY: 74354

African (AFR) AF: 0.259 AC: 10726 AN: 41468

American (AMR) AF: 0.339 AC: 5181 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3468

East Asian (EAS) AF: 0.573 AC: 2970 AN: 5182

South Asian (SAS) AF: 0.303 AC: 1457 AN: 4812

European-Finnish (FIN) AF: 0.246 AC: 2601 AN: 10586

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15973 AN: 67984

Other (OTH) AF: 0.274 AC: 579 AN: 2114

Alfa AF: 0.260 Hom.: 2217

Bravo AF: 0.276

Asia WGS AF: 0.415 AC: 1443 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.66
DANN	Benign	0.83
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs4128492; hg19: chr6-157768581; COSMIC: COSV60297290;