rs735860

Positions:

• chr6-53258320-T-C
• chr6-53258320-T-G

Variant summary

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

The XR_007059612.1(LOC124901332):​n.1102+3382A>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 0.659 in 152,064 control chromosomes in the GnomAD database, including 35,220 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 0.66 (35220 hom., cov: 31)
• Consequence: LOC124901332 XR_007059612.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692

Genes affected

LOC124901332 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901332	XR_007059612.1	n.1102+3382A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100134 AN: 151946 Hom.: 35160 Cov.: 31

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.659 AC: 100255 AN: 152064 Hom.: 35220 Cov.: 31 AF XY: 0.650 AC XY: 48273 AN XY: 74320

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.678

Alfa AF: 0.588 Hom.: 48968

Bravo AF: 0.690

Asia WGS AF: 0.567 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.5
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs735860; hg19: chr6-53123118;