rs1295652

Variant names:

• chr1-226865100-G-A
• rs1295652
• ENST00000834471.1:n.155-3383C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-226865100-G-A
• chr1-226865100-G-C

Variant summary

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

The ENST00000834471.1(ENSG00000308473):​n.155-3383C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,136 control chromosomes in the GnomAD database, including 4,424 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 0.24 (4424 hom., cov: 32)
• Consequence: ENSG00000308473 ENST00000834471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 7 publications found

Genes affected

ENSG00000308473 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373119	XR_949226.4	n.190-3383C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308473	ENST00000834471.1	n.155-3383C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35852 AN: 152018 Hom.: 4420 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.236 AC: 35870 AN: 152136 Hom.: 4424 Cov.: 32 AF XY: 0.236 AC XY: 17579 AN XY: 74386

African (AFR) AF: 0.230 AC: 9525 AN: 41480

American (AMR) AF: 0.252 AC: 3852 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 808 AN: 3472

East Asian (EAS) AF: 0.425 AC: 2204 AN: 5180

South Asian (SAS) AF: 0.263 AC: 1270 AN: 4824

European-Finnish (FIN) AF: 0.210 AC: 2222 AN: 10582

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15178 AN: 67984

Other (OTH) AF: 0.243 AC: 514 AN: 2116

Alfa AF: 0.201 Hom.: 1507

Bravo AF: 0.235

Asia WGS AF: 0.311 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.31
DANN	Benign	0.65
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1295652; hg19: chr1-227052801;