rs156244

Variant names:

• chr6-104416388-C-A
• rs156244
• ENST00000790145.1:n.408+4455C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-104416388-C-A
• chr6-104416388-C-G
• chr6-104416388-C-T

Variant summary

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

The ENST00000790145.1(ENSG00000302865):​n.408+4455C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.942 in 152,134 control chromosomes in the GnomAD database, including 68,076 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 0.94 (68076 hom., cov: 31)
• Consequence: ENSG00000302865 ENST00000790145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 2 publications found

Genes affected

ENSG00000302865 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 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
ENSG00000302865	ENST00000790145.1	n.408+4455C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.942 AC: 143225 AN: 152016 Hom.: 68054 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.981

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.942 AC: 143291 AN: 152134 Hom.: 68076 Cov.: 31 AF XY: 0.943 AC XY: 70163 AN XY: 74382

African (AFR) AF: 0.798 AC: 33047 AN: 41438

American (AMR) AF: 0.980 AC: 14986 AN: 15294

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5160 AN: 5160

South Asian (SAS) AF: 0.998 AC: 4806 AN: 4814

European-Finnish (FIN) AF: 1.00 AC: 10610 AN: 10610

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 67994 AN: 68024

Other (OTH) AF: 0.953 AC: 2016 AN: 2116

Alfa AF: 0.965 Hom.: 8852

Bravo AF: 0.934

Asia WGS AF: 0.986 AC: 3430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.70
DANN	Benign	0.50
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs156244; hg19: chr6-104864263;