rs1951923

Variant names:

• chr6-18352925-G-A
• rs1951923
• ENST00000790360.1:n.722-29971G>A

Variant summary

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

The ENST00000790360.1(ENSG00000289097):​n.722-29971G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,010 control chromosomes in the GnomAD database, including 7,772 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 0.31 (7772 hom., cov: 32)
• Consequence: ENSG00000289097 ENST00000790360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.842
• Publications: 7 publications found

Genes affected

ENSG00000289097 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790360.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289097	ENST00000790360.1		n.722-29971G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47380 AN: 151892 Hom.: 7769 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.312 AC: 47395 AN: 152010 Hom.: 7772 Cov.: 32 AF XY: 0.311 AC XY: 23114 AN XY: 74264

African (AFR) AF: 0.221 AC: 9181 AN: 41452

American (AMR) AF: 0.254 AC: 3879 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1230 AN: 3468

East Asian (EAS) AF: 0.416 AC: 2149 AN: 5164

South Asian (SAS) AF: 0.232 AC: 1118 AN: 4822

European-Finnish (FIN) AF: 0.367 AC: 3864 AN: 10536

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24684 AN: 67990

Other (OTH) AF: 0.326 AC: 690 AN: 2114

Alfa AF: 0.340 Hom.: 3587

Bravo AF: 0.302

Asia WGS AF: 0.329 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.7
DANN	Benign	0.73
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs1951923; hg19: chr6-18353156;