rs10955242

Variant names:

• chr8-100801402-G-A
• rs10955242
• ENST00000822257.1:n.235+4586G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-100801402-G-A
• chr8-100801402-G-C
• chr8-100801402-G-T

Variant summary

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

The ENST00000822257.1(ENSG00000306968):​n.235+4586G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,126 control chromosomes in the GnomAD database, including 1,902 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 0.13 (1902 hom., cov: 31)
• Consequence: ENSG00000306968 ENST00000822257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 2 publications found

Genes affected

ENSG00000306968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 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
ENSG00000306968	ENST00000822257.1	n.235+4586G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19640 AN: 152008 Hom.: 1890 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.0808

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.130 AC: 19701 AN: 152126 Hom.: 1902 Cov.: 31 AF XY: 0.133 AC XY: 9876 AN XY: 74390

African (AFR) AF: 0.233 AC: 9650 AN: 41484

American (AMR) AF: 0.201 AC: 3066 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0622 AC: 216 AN: 3472

East Asian (EAS) AF: 0.315 AC: 1630 AN: 5170

South Asian (SAS) AF: 0.0813 AC: 392 AN: 4824

European-Finnish (FIN) AF: 0.0562 AC: 596 AN: 10600

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0564 AC: 3836 AN: 67988

Other (OTH) AF: 0.122 AC: 256 AN: 2100

Alfa AF: 0.0664 Hom.: 121

Bravo AF: 0.148

Asia WGS AF: 0.180 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.6
DANN	Benign	0.76
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs10955242; hg19: chr8-101813630;