rs6976843

Positions:

• chr7-33063691-C-T

Variant summary

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

The XR_007060277.1(LOC124901610):​n.464+43C>T 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 0.32 in 152,026 control chromosomes in the GnomAD database, including 8,082 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 0.32 (8082 hom., cov: 32)
• Consequence: LOC124901610 XR_007060277.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

LOC124901610 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901610	XR_007060277.1	n.464+43C>T		intron_variant, non_coding_transcript_variant
LOC124901610	XR_007060278.1	n.464+43C>T		intron_variant, non_coding_transcript_variant
LOC124901610	XR_007060279.1	n.464+43C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48568 AN: 151908 Hom.: 8079 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.320 AC: 48612 AN: 152026 Hom.: 8082 Cov.: 32 AF XY: 0.319 AC XY: 23670 AN XY: 74294

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.285

Alfa AF: 0.344 Hom.: 1327

Bravo AF: 0.301

Asia WGS AF: 0.244 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.1
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6976843; hg19: chr7-33103303;