rs1562900

Variant names:

• chr2-21723567-T-C
• rs1562900
• ENST00000435237.1:n.194-75790T>C

Variant summary

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

The ENST00000435237.1(ENSG00000231204):​n.194-75790T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,028 control chromosomes in the GnomAD database, including 2,179 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 0.15 (2179 hom., cov: 32)
• Consequence: ENSG00000231204 ENST00000435237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.75
• Publications: 1 publications found

Genes affected

ENSG00000231204 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435237.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231204	ENST00000435237.1	TSL:3	n.194-75790T>C		intron	N/A
	ENSG00000231204	ENST00000717099.1		n.556-75790T>C		intron	N/A
	ENSG00000231204	ENST00000753412.1		n.74-3827T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22379 AN: 151910 Hom.: 2160 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0527

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0659

Gnomad SAS AF: 0.0960

Gnomad FIN AF: 0.0670

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.148 AC: 22435 AN: 152028 Hom.: 2179 Cov.: 32 AF XY: 0.145 AC XY: 10752 AN XY: 74322

African (AFR) AF: 0.272 AC: 11291 AN: 41464

American (AMR) AF: 0.123 AC: 1871 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3468

East Asian (EAS) AF: 0.0658 AC: 338 AN: 5136

South Asian (SAS) AF: 0.0955 AC: 460 AN: 4818

European-Finnish (FIN) AF: 0.0670 AC: 710 AN: 10598

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6887 AN: 67968

Other (OTH) AF: 0.155 AC: 327 AN: 2110

Alfa AF: 0.113 Hom.: 580

Bravo AF: 0.158

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.082
DANN	Benign	0.59
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1562900; hg19: chr2-21946439;