7-64290139-T-C

Position:

• chr7-64290139-T-C

Variant summary

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

The XR_927595.2(LOC105375323):​n.247-583A>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 0.145 in 151,870 control chromosomes in the GnomAD database, including 3,461 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 0.15 (3461 hom., cov: 33)
• Consequence: LOC105375323 XR_927595.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

Genes affected

LOC105375323 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375323	XR_927595.2	n.247-583A>G		intron_variant, non_coding_transcript_variant
LOC105375323	XR_001745021.1	n.52A>G		non_coding_transcript_exon_variant	1/4
LOC105375323	XR_927597.2	n.247-583A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21983 AN: 151748 Hom.: 3436 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.0683

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.000590

Gnomad SAS AF: 0.0135

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.0769

Gnomad NFE AF: 0.0535

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.145 AC: 22048 AN: 151870 Hom.: 3461 Cov.: 33 AF XY: 0.140 AC XY: 10387 AN XY: 74224

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.0682

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.000591

Gnomad4 SAS AF: 0.0131

Gnomad4 FIN AF: 0.0256

Gnomad4 NFE AF: 0.0535

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0875 Hom.: 714

Bravo AF: 0.160

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6960379; hg19: chr7-63750517;