chr6-153703805-C-G

Variant names:

• chr6-153703805-C-G
• rs1937596
• ENST00000765538.1:n.182-3674G>C

Variant summary

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

The ENST00000765538.1(ENSG00000299669):​n.182-3674G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,812 control chromosomes in the GnomAD database, including 10,097 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 0.35 (10097 hom., cov: 32)
• Consequence: ENSG00000299669 ENST00000765538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 2 publications found

Genes affected

ENSG00000299669 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 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
ENSG00000299669	ENST00000765538.1	n.182-3674G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53758 AN: 151694 Hom.: 10083 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.354 AC: 53803 AN: 151812 Hom.: 10097 Cov.: 32 AF XY: 0.351 AC XY: 26019 AN XY: 74164

African (AFR) AF: 0.474 AC: 19654 AN: 41436

American (AMR) AF: 0.391 AC: 5941 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1314 AN: 3456

East Asian (EAS) AF: 0.242 AC: 1245 AN: 5154

South Asian (SAS) AF: 0.241 AC: 1161 AN: 4822

European-Finnish (FIN) AF: 0.312 AC: 3292 AN: 10538

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19948 AN: 67890

Other (OTH) AF: 0.373 AC: 784 AN: 2104

Alfa AF: 0.161 Hom.: 277

Bravo AF: 0.373

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.20
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1937596; hg19: chr6-154024940;