chr5-107775475-G-T

Variant names:

• chr5-107775475-G-T
• rs1422438
• ENST00000737254.1:n.292+2579G>T

Variant summary

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

The ENST00000737254.1(ENSG00000296200):​n.292+2579G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,058 control chromosomes in the GnomAD database, including 29,711 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 0.61 (29711 hom., cov: 32)
• Consequence: ENSG00000296200 ENST00000737254.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 5 publications found

Genes affected

ENSG00000296200 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 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
ENSG00000296200	ENST00000737254.1	n.292+2579G>T		intron_variant	Intron 1 of 2
ENSG00000296200	ENST00000737255.1	n.257+2579G>T		intron_variant	Intron 1 of 1
ENSG00000296200	ENST00000737256.1	n.250+2579G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93152 AN: 151940 Hom.: 29688 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.613 AC: 93201 AN: 152058 Hom.: 29711 Cov.: 32 AF XY: 0.610 AC XY: 45344 AN XY: 74328

African (AFR) AF: 0.437 AC: 18113 AN: 41456

American (AMR) AF: 0.622 AC: 9510 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2750 AN: 3472

East Asian (EAS) AF: 0.506 AC: 2606 AN: 5150

South Asian (SAS) AF: 0.651 AC: 3138 AN: 4822

European-Finnish (FIN) AF: 0.653 AC: 6901 AN: 10570

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47778 AN: 67992

Other (OTH) AF: 0.660 AC: 1393 AN: 2112

Alfa AF: 0.662 Hom.: 79759

Bravo AF: 0.601

Asia WGS AF: 0.598 AC: 2082 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.29
DANN	Benign	0.47
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs1422438; hg19: chr5-107111176; COSMIC: COSV60179856;