5-7368732-C-T

Position:

• chr5-7368732-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000513219.1(ENSG00000249865):​n.275+701G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0918 in 152,154 control chromosomes in the GnomAD database, including 719 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 0.092 (719 hom., cov: 32)
• Consequence: ENST00000513219.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374645	XR_925758.3	n.388+701G>A		intron_variant, non_coding_transcript_variant
LOC105374645	XR_925756.3	n.394+701G>A		intron_variant, non_coding_transcript_variant
LOC105374645	XR_925760.4	n.394+701G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000513219.1	n.275+701G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0918 AC: 13962 AN: 152034 Hom.: 718 Cov.: 32

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0647

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0175

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0991

Gnomad OTH AF: 0.0927

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

GnomAD4 genome AF: 0.0918 AC: 13969 AN: 152154 Hom.: 719 Cov.: 32 AF XY: 0.0920 AC XY: 6843 AN XY: 74380

Gnomad4 AFR AF: 0.0848

Gnomad4 AMR AF: 0.0645

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.0180

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.0992

Gnomad4 OTH AF: 0.0908

Alfa AF: 0.0897 Hom.: 830

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	10
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13172324; hg19: chr5-7368845;