ENST00000775945.1:n.381+19265T>C

Variant names:

• chr5-149697425-T-C
• rs7713955
• ENST00000775945.1:n.381+19265T>C

Variant summary

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

The ENST00000775945.1(ENSG00000301068):​n.381+19265T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,146 control chromosomes in the GnomAD database, including 51,454 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 0.82 (51454 hom., cov: 32)
• Consequence: ENSG00000301068 ENST00000775945.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 2 publications found

Genes affected

ENSG00000301068 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.882 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
ENSG00000301068	ENST00000775945.1	n.381+19265T>C		intron_variant	Intron 1 of 1
ENSG00000301068	ENST00000775946.1	n.152-6520T>C		intron_variant	Intron 1 of 2
ENSG00000301068	ENST00000775947.1	n.146+13086T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124733 AN: 152028 Hom.: 51387 Cov.: 32

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.821 AC: 124861 AN: 152146 Hom.: 51454 Cov.: 32 AF XY: 0.822 AC XY: 61160 AN XY: 74374

African (AFR) AF: 0.890 AC: 36921 AN: 41504

American (AMR) AF: 0.822 AC: 12568 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2754 AN: 3472

East Asian (EAS) AF: 0.775 AC: 4014 AN: 5182

South Asian (SAS) AF: 0.899 AC: 4333 AN: 4818

European-Finnish (FIN) AF: 0.814 AC: 8611 AN: 10576

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.780 AC: 53038 AN: 67996

Other (OTH) AF: 0.800 AC: 1688 AN: 2110

Alfa AF: 0.814 Hom.: 8410

Bravo AF: 0.820

Asia WGS AF: 0.876 AC: 3045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.46
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7713955; hg19: chr5-149076988; COSMIC: COSV68555128;