rs10435419

Positions:

• chr7-134645607-A-C

Variant summary

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

The XR_007060537.1(LOC124901750):​n.29222-25659T>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 0.0284 in 152,308 control chromosomes in the GnomAD database, including 94 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 0.028 (94 hom., cov: 33)
• Consequence: LOC124901750 XR_007060537.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

Genes affected

LOC124901750 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901750	XR_007060537.1	n.29222-25659T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0284 AC: 4319 AN: 152190 Hom.: 90 Cov.: 33

Gnomad AFR AF: 0.0246

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0489

Gnomad FIN AF: 0.0140

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0209

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0284 AC: 4325 AN: 152308 Hom.: 94 Cov.: 33 AF XY: 0.0293 AC XY: 2179 AN XY: 74470

Gnomad4 AFR AF: 0.0246

Gnomad4 AMR AF: 0.0519

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.0481

Gnomad4 FIN AF: 0.0140

Gnomad4 NFE AF: 0.0209

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.0321 Hom.: 43

Bravo AF: 0.0339

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	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: rs10435419; hg19: chr7-134330359;