5-73255307-A-G

Position:

• chr5-73255307-A-G

Variant summary

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

The ENST00000654696.1(ENSG00000249743):​n.353-31180A>G 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 0.409 in 151,818 control chromosomes in the GnomAD database, including 13,319 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 0.41 (13319 hom., cov: 31)
• Consequence: ENST00000654696.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901002	XR_007058818.1	n.347-31180A>G		intron_variant, non_coding_transcript_variant
LOC105379031	XR_948470.3	n.246-8651T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654696.1	n.353-31180A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62022 AN: 151700 Hom.: 13295 Cov.: 31

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.409 AC: 62095 AN: 151818 Hom.: 13319 Cov.: 31 AF XY: 0.404 AC XY: 29942 AN XY: 74180

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.404

Alfa AF: 0.385 Hom.: 26112

Bravo AF: 0.412

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.83
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7702331; hg19: chr5-72551134;