rs2030926

Variant names:

• chr6-113745925-T-C
• rs2030926
• ENST00000806291.1:n.571-4410T>C

Variant summary

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

The ENST00000806291.1(ENSG00000304785):​n.571-4410T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,948 control chromosomes in the GnomAD database, including 16,876 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 0.47 (16876 hom., cov: 31)
• Consequence: ENSG00000304785 ENST00000806291.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551
• Publications: 9 publications found

Genes affected

ENSG00000304785 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 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
ENSG00000304785	ENST00000806291.1	n.571-4410T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71049 AN: 151832 Hom.: 16875 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.468 AC: 71086 AN: 151948 Hom.: 16876 Cov.: 31 AF XY: 0.461 AC XY: 34234 AN XY: 74234

African (AFR) AF: 0.510 AC: 21144 AN: 41450

American (AMR) AF: 0.406 AC: 6202 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1891 AN: 3466

East Asian (EAS) AF: 0.479 AC: 2469 AN: 5156

South Asian (SAS) AF: 0.443 AC: 2133 AN: 4810

European-Finnish (FIN) AF: 0.380 AC: 4001 AN: 10534

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.466 AC: 31693 AN: 67960

Other (OTH) AF: 0.491 AC: 1036 AN: 2110

Alfa AF: 0.469 Hom.: 29528

Bravo AF: 0.472

Asia WGS AF: 0.452 AC: 1573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.72
DANN	Benign	0.76
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2030926; hg19: chr6-114067127; COSMIC: COSV69420875;