rs1904173

Variant names:

• chr5-25419980-G-A
• rs1904173
• ENST00000507887.6:n.239+2750C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-25419980-G-A
• chr5-25419980-G-C
• chr5-25419980-G-T

Variant summary

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

The ENST00000507887.6(ENSG00000248605):​n.239+2750C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,002 control chromosomes in the GnomAD database, including 2,442 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 0.17 (2442 hom., cov: 32)
• Consequence: ENSG00000248605 ENST00000507887.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 3 publications found

Genes affected

ENSG00000248605 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507887.6. 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
	ENSG00000248605	ENST00000507887.6	TSL:3	n.239+2750C>T		intron	N/A
	ENSG00000248605	ENST00000507926.2	TSL:5	n.232+2750C>T		intron	N/A
	ENSG00000248605	ENST00000511029.5	TSL:3	n.126+2750C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25599 AN: 151884 Hom.: 2431 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.0811

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.169 AC: 25625 AN: 152002 Hom.: 2442 Cov.: 32 AF XY: 0.168 AC XY: 12499 AN XY: 74280

African (AFR) AF: 0.248 AC: 10295 AN: 41460

American (AMR) AF: 0.105 AC: 1598 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3468

East Asian (EAS) AF: 0.000775 AC: 4 AN: 5164

South Asian (SAS) AF: 0.0806 AC: 387 AN: 4802

European-Finnish (FIN) AF: 0.245 AC: 2582 AN: 10552

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9959 AN: 67960

Other (OTH) AF: 0.125 AC: 264 AN: 2106

Alfa AF: 0.148 Hom.: 5394

Bravo AF: 0.161

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.70
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1904173; hg19: chr5-25420089;