rs205610

Variant names:

• chr2-74745479-G-T
• rs205610
• ENST00000674157.1:n.318-3826C>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000674157.1(ENSG00000287687):​n.318-3826C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00506 in 151,592 control chromosomes in the GnomAD database, including 6 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 0.0051 (6 hom., cov: 33)
• Consequence: ENSG00000287687 ENST00000674157.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14
• Publications: 1 publications found

Genes affected

ENSG00000287687 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BS2: High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724497	XR_001739541.2	n.515-9083G>T		intron_variant	Intron 2 of 2
LOC102724497	XR_001739542.2	n.952-9083G>T		intron_variant	Intron 2 of 2
LOC102724497	XR_427047.5	n.138-9083G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287687	ENST00000674157.1	n.318-3826C>A		intron_variant	Intron 1 of 4
ENSG00000286739	ENST00000690069.2	n.245-9083G>T		intron_variant	Intron 2 of 3
ENSG00000286739	ENST00000744070.1	n.184-9083G>T		intron_variant	Intron 2 of 3
ENSG00000286739	ENST00000744071.1	n.199-9083G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.00506 AC: 767 AN: 151476 Hom.: 6 Cov.: 33

Gnomad AFR AF: 0.00100

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000525

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00146

Gnomad FIN AF: 0.0185

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00750

Gnomad OTH AF: 0.00144

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

GnomAD4 genome AF: 0.00506 AC: 767 AN: 151592 Hom.: 6 Cov.: 33 AF XY: 0.00529 AC XY: 392 AN XY: 74144

African (AFR) AF: 0.000998 AC: 41 AN: 41090

American (AMR) AF: 0.000524 AC: 8 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00146 AC: 7 AN: 4800

European-Finnish (FIN) AF: 0.0185 AC: 196 AN: 10622

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.00750 AC: 509 AN: 67844

Other (OTH) AF: 0.00142 AC: 3 AN: 2106

Alfa AF: 0.00895 Hom.: 1

Bravo AF: 0.00306

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	13
DANN	Benign	0.73
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs205610; hg19: chr2-74972606;