rs4422679

Positions:

• chr7-11910321-A-G
• chr7-11910321-A-T

Variant summary

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

The XR_007060211.1(LOC124901589):​n.86-16935T>C 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 0.427 in 152,094 control chromosomes in the GnomAD database, including 15,017 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 0.43 (15017 hom., cov: 32)
• Consequence: LOC124901589 XR_007060211.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

Genes affected

LOC124901589 (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 (EAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901589	XR_007060211.1	n.86-16935T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64808 AN: 151976 Hom.: 14987 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.427 AC: 64899 AN: 152094 Hom.: 15017 Cov.: 32 AF XY: 0.428 AC XY: 31845 AN XY: 74340

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.406

Alfa AF: 0.403 Hom.: 2086

Bravo AF: 0.446

Asia WGS AF: 0.544 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.3
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: rs4422679; hg19: chr7-11949947;