rs7730710

chr5-101576739-A-G

Variant summary

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

The XR_007058891.1(LOC105379102):n.549+14898T>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 0.0637 in 152,308 control chromosomes in the GnomAD database, including 855 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 0.064 (855 hom., cov: 32)
• Consequence: LOC105379102 XR_007058891.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

Genes affected

LOC105379102 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379102	XR_007058891.1	n.549+14898T>C		intron_variant, non_coding_transcript_variant
LOC105379102	XR_001742829.2	n.286+14898T>C		intron_variant, non_coding_transcript_variant
LOC105379102	XR_948628.3	n.549+14898T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0636 AC: 9685 AN: 152190 Hom.: 853 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0317

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00496

Gnomad FIN AF: 0.000376

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00910

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0637 AC: 9707 AN: 152308 Hom.: 855 Cov.: 32 AF XY: 0.0617 AC XY: 4597 AN XY: 74474

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.0317

Gnomad4 ASJ AF: 0.0291

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00476

Gnomad4 FIN AF: 0.000376

Gnomad4 NFE AF: 0.00910

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0288 Hom.: 112

Bravo AF: 0.0738

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.5
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7730710; hg19: chr5-100912443;