rs7703021

chr5-92635591-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000512210.5(ENSG00000249776):n.52+3855T>C 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 0.144 in 152,158 control chromosomes in the GnomAD database, including 1,721 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 0.14 (1721 hom., cov: 32)
• Consequence: ENST00000512210.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379082	XR_001742809.2	n.217+35893T>C		intron_variant, non_coding_transcript_variant
LOC105379082	XR_001742810.2	n.397+34161T>C		intron_variant, non_coding_transcript_variant
LOC105379082	XR_948566.3	n.362+34161T>C		intron_variant, non_coding_transcript_variant
LOC105379082	XR_948568.3	n.365+34161T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000512210.5	n.52+3855T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000513779.1	n.134+25139T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21925 AN: 152042 Hom.: 1719 Cov.: 32

Gnomad AFR AF: 0.0745

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0284

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.144 AC: 21925 AN: 152158 Hom.: 1721 Cov.: 32 AF XY: 0.142 AC XY: 10531 AN XY: 74388

Gnomad4 AFR AF: 0.0744

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0286

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.161

Alfa AF: 0.176 Hom.: 1444

Bravo AF: 0.147

Asia WGS AF: 0.121 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
Cadd	Benign	16
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7703021; hg19: chr5-91971298;