rs2505997

Variant names:

• chr10-43074907-C-T
• rs2505997
• ENST00000794440.1:n.51+2154G>A

Variant summary

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

The ENST00000794440.1(ENSG00000303432):​n.51+2154G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,170 control chromosomes in the GnomAD database, including 7,955 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 0.32 (7955 hom., cov: 33)
• Consequence: ENSG00000303432 ENST00000794440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 3 publications found

Genes affected

ENSG00000303432 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 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
ENSG00000303432	ENST00000794440.1	n.51+2154G>A		intron_variant	Intron 1 of 2
ENSG00000303432	ENST00000794441.1	n.116+2126G>A		intron_variant	Intron 1 of 3
ENSG00000303432	ENST00000794442.1	n.107+2126G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48633 AN: 152050 Hom.: 7927 Cov.: 33

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.320 AC: 48706 AN: 152170 Hom.: 7955 Cov.: 33 AF XY: 0.318 AC XY: 23649 AN XY: 74396

African (AFR) AF: 0.363 AC: 15090 AN: 41524

American (AMR) AF: 0.373 AC: 5702 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 946 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1642 AN: 5172

South Asian (SAS) AF: 0.347 AC: 1675 AN: 4824

European-Finnish (FIN) AF: 0.198 AC: 2104 AN: 10606

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20460 AN: 67960

Other (OTH) AF: 0.336 AC: 711 AN: 2114

Alfa AF: 0.304 Hom.: 1975

Bravo AF: 0.335

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.66
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2505997; hg19: chr10-43570355;