rs1916961

Positions:

• chr2-188727157-G-A
• chr2-188727157-G-C
• chr2-188727157-G-T

Variant summary

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

The ENST00000431708.1(ENSG00000223523):​n.218+19267C>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 0.895 in 151,950 control chromosomes in the GnomAD database, including 61,159 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 0.90 (61159 hom., cov: 31)
• Consequence: ENST00000431708.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373790	XR_923685.3	n.112-11435G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000431708.1	n.218+19267C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.896 AC: 135977 AN: 151832 Hom.: 61122 Cov.: 31

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.895 AC: 136070 AN: 151950 Hom.: 61159 Cov.: 31 AF XY: 0.896 AC XY: 66561 AN XY: 74286

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.913

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.977

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.903

Alfa AF: 0.908 Hom.: 122505

Bravo AF: 0.892

Asia WGS AF: 0.981 AC: 3410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1916961; hg19: chr2-189591884;