rs10185704

Variant names:

• chr2-173436295-T-C
• rs10185704
• ENST00000841881.1:n.378-302A>G

Variant summary

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

The ENST00000841881.1(ENSG00000309536):​n.378-302A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,038 control chromosomes in the GnomAD database, including 5,181 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 0.26 (5181 hom., cov: 32)
• Consequence: ENSG00000309536 ENST00000841881.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990
• Publications: 1 publications found

Genes affected

ENSG00000309536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841881.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309536	ENST00000841881.1		n.378-302A>G		intron	N/A
	ENSG00000309536	ENST00000841882.1		n.171-302A>G		intron	N/A
	ENSG00000309536	ENST00000841883.1		n.141-144A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39155 AN: 151920 Hom.: 5173 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.258 AC: 39192 AN: 152038 Hom.: 5181 Cov.: 32 AF XY: 0.260 AC XY: 19312 AN XY: 74328

African (AFR) AF: 0.215 AC: 8893 AN: 41438

American (AMR) AF: 0.301 AC: 4604 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 777 AN: 3468

East Asian (EAS) AF: 0.379 AC: 1960 AN: 5170

South Asian (SAS) AF: 0.202 AC: 972 AN: 4812

European-Finnish (FIN) AF: 0.266 AC: 2810 AN: 10574

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18349 AN: 67972

Other (OTH) AF: 0.242 AC: 511 AN: 2114

Alfa AF: 0.255 Hom.: 643

Bravo AF: 0.264

Asia WGS AF: 0.251 AC: 872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.56
DANN	Benign	0.36
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs10185704; hg19: chr2-174301023;