rs7993057

chr13-42724916-G-Achr13-42724916-G-C

Variant summary

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

The XR_007063769.1(LOC124903164):n.671-4215C>T 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 0.932 in 152,272 control chromosomes in the GnomAD database, including 66,568 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 0.93 (66568 hom., cov: 33)
• Consequence: LOC124903164 XR_007063769.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837

Genes affected

LOC124903164 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903164	XR_007063769.1	n.671-4215C>T		intron_variant, non_coding_transcript_variant
LOC124903164	XM_047430822.1	c.131-4215C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.933 AC: 141889 AN: 152154 Hom.: 66536 Cov.: 33

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.964

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.983

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.980

Gnomad OTH AF: 0.946

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

GnomAD4 genome AF: 0.932 AC: 141978 AN: 152272 Hom.: 66568 Cov.: 33 AF XY: 0.934 AC XY: 69513 AN XY: 74450

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.964

Gnomad4 ASJ AF: 0.989

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.983

Gnomad4 FIN AF: 0.972

Gnomad4 NFE AF: 0.980

Gnomad4 OTH AF: 0.945

Alfa AF: 0.960 Hom.: 27938

Bravo AF: 0.928

Asia WGS AF: 0.954 AC: 3318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.20
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7993057; hg19: chr13-43299052;