rs1550623

chr2-173348166-G-Achr2-173348166-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000437243.1(ENSG00000293276):n.42+8001C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,096 control chromosomes in the GnomAD database, including 49,762 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 0.81 (49762 hom., cov: 32)
• Consequence: ENST00000437243.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000437243.1	n.42+8001C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122405 AN: 151978 Hom.: 49722 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.805 AC: 122491 AN: 152096 Hom.: 49762 Cov.: 32 AF XY: 0.807 AC XY: 59990 AN XY: 74338

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.819

Alfa AF: 0.833 Hom.: 32615

Bravo AF: 0.793

Asia WGS AF: 0.926 AC: 3222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.8
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1550623; hg19: chr2-174212894;