rs1365965

Variant names:

• chr2-203887147-T-C
• rs1365965
• ENST00000810800.1:n.63+6328T>C

Variant summary

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

The ENST00000810800.1(ENSG00000305408):​n.63+6328T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,950 control chromosomes in the GnomAD database, including 10,974 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 0.37 (10974 hom., cov: 31)
• Consequence: ENSG00000305408 ENST00000810800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 8 publications found

Genes affected

ENSG00000305408 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 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
ENSG00000305408	ENST00000810800.1	n.63+6328T>C		intron_variant	Intron 1 of 2
ENSG00000305408	ENST00000810801.1	n.83+6328T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56292 AN: 151832 Hom.: 10962 Cov.: 31

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.371 AC: 56351 AN: 151950 Hom.: 10974 Cov.: 31 AF XY: 0.376 AC XY: 27955 AN XY: 74264

African (AFR) AF: 0.416 AC: 17229 AN: 41432

American (AMR) AF: 0.387 AC: 5911 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 865 AN: 3466

East Asian (EAS) AF: 0.592 AC: 3059 AN: 5164

South Asian (SAS) AF: 0.229 AC: 1105 AN: 4816

European-Finnish (FIN) AF: 0.488 AC: 5143 AN: 10546

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.323 AC: 21960 AN: 67942

Other (OTH) AF: 0.319 AC: 674 AN: 2114

Alfa AF: 0.342 Hom.: 1860

Bravo AF: 0.370

Asia WGS AF: 0.373 AC: 1293 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	9.6
DANN	Benign	0.66
PhyloP100		-0.093

Splicing

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

Other links and lift over

dbSNP: rs1365965; hg19: chr2-204751870;