chr6-141604867-C-T

Variant names:

• chr6-141604867-C-T
• rs34596385
• ENST00000847688.1:n.206-12116C>T

Variant summary

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

The ENST00000847688.1(ENSG00000310155):​n.206-12116C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0403 in 152,048 control chromosomes in the GnomAD database, including 165 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 0.040 (165 hom., cov: 32)
• Consequence: ENSG00000310155 ENST00000847688.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 1 publications found

Genes affected

ENSG00000310155 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0572 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
ENSG00000310155	ENST00000847688.1	n.206-12116C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0403 AC: 6117 AN: 151928 Hom.: 165 Cov.: 32

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0317

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00373

Gnomad FIN AF: 0.0884

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.0413

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

GnomAD4 genome AF: 0.0403 AC: 6120 AN: 152048 Hom.: 165 Cov.: 32 AF XY: 0.0400 AC XY: 2975 AN XY: 74336

African (AFR) AF: 0.0117 AC: 484 AN: 41478

American (AMR) AF: 0.0316 AC: 483 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 92 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.00394 AC: 19 AN: 4820

European-Finnish (FIN) AF: 0.0884 AC: 934 AN: 10566

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0587 AC: 3993 AN: 67970

Other (OTH) AF: 0.0408 AC: 86 AN: 2106

Alfa AF: 0.0484 Hom.: 44

Bravo AF: 0.0356

Asia WGS AF: 0.00433 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.62
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs34596385; hg19: chr6-141926004;