rs1004561

Positions:

• chr7-96795015-T-A
• chr7-96795015-T-C
• chr7-96795015-T-G

Variant summary

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

The XR_927783.2(LOC105375414):​n.263+5216T>A 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 0.0429 in 152,270 control chromosomes in the GnomAD database, including 195 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 0.043 (195 hom., cov: 33)
• Consequence: LOC105375414 XR_927783.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71

Genes affected

LOC105375414 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375414	XR_927783.2	n.263+5216T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0429 AC: 6528 AN: 152152 Hom.: 195 Cov.: 33

Gnomad AFR AF: 0.0100

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0340

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.0435

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0570

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0608

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0429 AC: 6525 AN: 152270 Hom.: 195 Cov.: 33 AF XY: 0.0427 AC XY: 3181 AN XY: 74452

Gnomad4 AFR AF: 0.00999

Gnomad4 AMR AF: 0.0339

Gnomad4 ASJ AF: 0.0839

Gnomad4 EAS AF: 0.0438

Gnomad4 SAS AF: 0.0377

Gnomad4 FIN AF: 0.0570

Gnomad4 NFE AF: 0.0608

Gnomad4 OTH AF: 0.0459

Alfa AF: 0.0232 Hom.: 13

Bravo AF: 0.0397

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	15
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1004561; hg19: chr7-96424327;