rs1899965

Positions:

• chr4-143867045-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000641328.1(ENSG00000251600):​n.1315+969T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0168 in 152,240 control chromosomes in the GnomAD database, including 36 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 0.017 (36 hom., cov: 33)
• Consequence: ENSG00000251600 ENST00000641328.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

Genes affected

ENSG00000251600 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0168 (2563/152240) while in subpopulation NFE AF= 0.0244 (1657/68008). AF 95% confidence interval is 0.0234. There are 36 homozygotes in gnomad4. There are 1234 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 36 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377459	XR_001741861.1	n.1463+969T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000251600	ENST00000641328.1	n.1315+969T>C		intron_variant
ENSG00000251600	ENST00000641556.1	n.356+969T>C		intron_variant
ENSG00000251600	ENST00000641676.1	n.301+969T>C		intron_variant
ENSG00000251600	ENST00000664496.1	n.351+969T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0168 AC: 2563 AN: 152122 Hom.: 36 Cov.: 33

Gnomad AFR AF: 0.00478

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0146

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.0201

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0244

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0168 AC: 2563 AN: 152240 Hom.: 36 Cov.: 33 AF XY: 0.0166 AC XY: 1234 AN XY: 74428

Gnomad4 AFR AF: 0.00477

Gnomad4 AMR AF: 0.0146

Gnomad4 ASJ AF: 0.0329

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00291

Gnomad4 FIN AF: 0.0201

Gnomad4 NFE AF: 0.0244

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.0212 Hom.: 4

Bravo AF: 0.0160

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1899965; hg19: chr4-144788198;