rs113795410

Variant names:

• chr6-29760432-C-A
• rs113795410
• ENST00000648999.1:n.356-1342C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-29760432-C-A
• chr6-29760432-C-G
• chr6-29760432-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648999.1(ENSG00000285761):​n.356-1342C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,186 control chromosomes in the GnomAD database, including 51,080 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 0.82 (51080 hom., cov: 32)
• Consequence: ENSG00000285761 ENST00000648999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

Genes affected

ENSG00000285761 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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
ENSG00000285761	ENST00000648999.1	n.356-1342C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124188 AN: 152068 Hom.: 51019 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.817 AC: 124308 AN: 152186 Hom.: 51080 Cov.: 32 AF XY: 0.815 AC XY: 60617 AN XY: 74390

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.825

Alfa AF: 0.830 Hom.: 78410

Bravo AF: 0.828

Asia WGS AF: 0.939 AC: 3267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs113795410; hg19: chr6-29728209;