chr5-77913837-T-C

Variant names:

• chr5-77913837-T-C
• rs5014235
• ENST00000719931.1:n.340+6973A>G

Variant summary

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

The ENST00000719931.1(ENSG00000293921):​n.340+6973A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 152,020 control chromosomes in the GnomAD database, including 48,665 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 0.79 (48665 hom., cov: 30)
• Consequence: ENSG00000293921 ENST00000719931.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 4 publications found

Genes affected

ENSG00000293921 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929154	NR_105012.1	n.170+29012T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293921	ENST00000719931.1	n.340+6973A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120531 AN: 151900 Hom.: 48614 Cov.: 30

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.794 AC: 120642 AN: 152020 Hom.: 48665 Cov.: 30 AF XY: 0.795 AC XY: 59037 AN XY: 74258

African (AFR) AF: 0.945 AC: 39229 AN: 41512

American (AMR) AF: 0.819 AC: 12516 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2684 AN: 3472

East Asian (EAS) AF: 0.903 AC: 4620 AN: 5114

South Asian (SAS) AF: 0.734 AC: 3533 AN: 4814

European-Finnish (FIN) AF: 0.735 AC: 7755 AN: 10558

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47828 AN: 67958

Other (OTH) AF: 0.786 AC: 1659 AN: 2110

Alfa AF: 0.737 Hom.: 129712

Bravo AF: 0.811

Asia WGS AF: 0.806 AC: 2801 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	9.6
DANN	Benign	0.61
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs5014235; hg19: chr5-77209661;