chr5-103674067-C-T

Variant names:

• chr5-103674067-C-T
• rs11950651
• ENST00000750993.1:n.64-4445C>T

Variant summary

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

The ENST00000750993.1(ENSG00000297797):​n.64-4445C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0748 in 152,202 control chromosomes in the GnomAD database, including 710 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 0.075 (710 hom., cov: 33)
• Consequence: ENSG00000297797 ENST00000750993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85
• Publications: 1 publications found

Genes affected

ENSG00000297797 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379107	XR_001742831.2	n.150-4445C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297797	ENST00000750993.1	n.64-4445C>T		intron_variant	Intron 1 of 4
ENSG00000297797	ENST00000750994.1	n.30-4445C>T		intron_variant	Intron 1 of 4
ENSG00000297797	ENST00000750995.1	n.113-4445C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0749 AC: 11395 AN: 152084 Hom.: 715 Cov.: 33

Gnomad AFR AF: 0.0242

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0752

Gnomad OTH AF: 0.0732

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

GnomAD4 genome AF: 0.0748 AC: 11385 AN: 152202 Hom.: 710 Cov.: 33 AF XY: 0.0791 AC XY: 5885 AN XY: 74402

African (AFR) AF: 0.0241 AC: 1003 AN: 41542

American (AMR) AF: 0.0909 AC: 1389 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3470

East Asian (EAS) AF: 0.337 AC: 1741 AN: 5160

South Asian (SAS) AF: 0.152 AC: 730 AN: 4814

European-Finnish (FIN) AF: 0.0975 AC: 1033 AN: 10596

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0753 AC: 5119 AN: 68020

Other (OTH) AF: 0.0748 AC: 158 AN: 2112

Alfa AF: 0.0746 Hom.: 642

Bravo AF: 0.0729

Asia WGS AF: 0.235 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.037
DANN	Benign	0.68
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs11950651; hg19: chr5-103009768;