rs6748358

Variant names:

• chr2-203892182-C-A
• rs6748358
• ENST00000810800.1:n.64-4684C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-203892182-C-A
• chr2-203892182-C-T

Variant summary

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

The ENST00000810800.1(ENSG00000305408):​n.64-4684C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,964 control chromosomes in the GnomAD database, including 13,732 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 0.41 (13732 hom., cov: 31)
• Consequence: ENSG00000305408 ENST00000810800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833
• Publications: 18 publications found

Genes affected

ENSG00000305408 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.655 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
ENSG00000305408	ENST00000810800.1	n.64-4684C>A		intron_variant	Intron 1 of 2
ENSG00000305408	ENST00000810801.1	n.84-4684C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62481 AN: 151846 Hom.: 13738 Cov.: 31

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.411 AC: 62484 AN: 151964 Hom.: 13732 Cov.: 31 AF XY: 0.410 AC XY: 30414 AN XY: 74270

African (AFR) AF: 0.267 AC: 11047 AN: 41420

American (AMR) AF: 0.455 AC: 6948 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1837 AN: 3464

East Asian (EAS) AF: 0.297 AC: 1531 AN: 5160

South Asian (SAS) AF: 0.674 AC: 3249 AN: 4820

European-Finnish (FIN) AF: 0.342 AC: 3614 AN: 10568

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32709 AN: 67944

Other (OTH) AF: 0.472 AC: 996 AN: 2110

Alfa AF: 0.472 Hom.: 25937

Bravo AF: 0.406

Asia WGS AF: 0.509 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.55
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs6748358; hg19: chr2-204756905;