rs7251505

Variant names:

• chr19-33311636-G-A
• rs7251505
• ENST00000807661.1:n.124-5691C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-33311636-G-A
• chr19-33311636-G-T

Variant summary

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

The ENST00000807661.1(ENSG00000305011):​n.124-5691C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,212 control chromosomes in the GnomAD database, including 961 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 0.10 (961 hom., cov: 32)
• Consequence: ENSG00000305011 ENST00000807661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 12 publications found

Genes affected

ENSG00000305011 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305011	ENST00000807661.1	n.124-5691C>T		intron_variant	Intron 1 of 2
ENSG00000305011	ENST00000807662.1	n.88-5189C>T		intron_variant	Intron 1 of 3
ENSG00000305011	ENST00000807663.1	n.87-5679C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15294 AN: 152094 Hom.: 958 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0751

Gnomad ASJ AF: 0.0902

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0213

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0877

Gnomad OTH AF: 0.0989

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

GnomAD4 genome AF: 0.101 AC: 15315 AN: 152212 Hom.: 961 Cov.: 32 AF XY: 0.0974 AC XY: 7253 AN XY: 74438

African (AFR) AF: 0.170 AC: 7056 AN: 41516

American (AMR) AF: 0.0749 AC: 1145 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0902 AC: 313 AN: 3470

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5172

South Asian (SAS) AF: 0.0224 AC: 108 AN: 4826

European-Finnish (FIN) AF: 0.0413 AC: 438 AN: 10612

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0877 AC: 5966 AN: 68010

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.0758 Hom.: 292

Bravo AF: 0.106

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.83
DANN	Benign	0.36
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs7251505; hg19: chr19-33802542;