rs79811809

chr7-140933681-A-G

Variant summary

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

The XR_002956518.2(LOC105375536):n.1531-5706A>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 0.0607 in 152,270 control chromosomes in the GnomAD database, including 405 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 0.061 (405 hom., cov: 32)
• Consequence: LOC105375536 XR_002956518.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

LOC105375536 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375536	XR_002956518.2	n.1531-5706A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0607 AC: 9236 AN: 152152 Hom.: 405 Cov.: 32

Gnomad AFR AF: 0.0152

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0558

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0101

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0853

Gnomad OTH AF: 0.0597

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

GnomAD4 genome AF: 0.0607 AC: 9238 AN: 152270 Hom.: 405 Cov.: 32 AF XY: 0.0614 AC XY: 4571 AN XY: 74440

Gnomad4 AFR AF: 0.0152

Gnomad4 AMR AF: 0.0558

Gnomad4 ASJ AF: 0.0905

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0106

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0853

Gnomad4 OTH AF: 0.0591

Alfa AF: 0.0761 Hom.: 76

Bravo AF: 0.0534

Asia WGS AF: 0.00953 AC: 33 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.12
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs79811809; hg19: chr7-140633481;