rs6465475

Positions:

• chr7-95695555-T-A
• chr7-95695555-T-C

Variant summary

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

The XR_927774.3(LOC105375409):​n.177-21552T>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 0.277 in 151,506 control chromosomes in the GnomAD database, including 7,209 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 0.28 (7209 hom., cov: 32)
• Consequence: LOC105375409 XR_927774.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575

Genes affected

LOC105375409 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375409	XR_927774.3	n.177-21552T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 41942 AN: 151388 Hom.: 7193 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0630

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.277 AC: 42003 AN: 151506 Hom.: 7209 Cov.: 32 AF XY: 0.272 AC XY: 20148 AN XY: 74062

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.0627

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.276

Alfa AF: 0.103 Hom.: 140

Bravo AF: 0.287

Asia WGS AF: 0.162 AC: 563 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6465475; hg19: chr7-95324867;