7-142307367-AGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGT

Position:

• chr7-142307367-AGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.014 (18 hom., cov: 0)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0141 (2062/146288) while in subpopulation NFE AF= 0.0171 (1136/66364). AF 95% confidence interval is 0.0163. There are 18 homozygotes in gnomad4. There are 1026 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 18 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.142307368_142307369delGT		intergenic_region
TRB		n.142307399_142307400delTG		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0140 AC: 2051 AN: 146182 Hom.: 16 Cov.: 0

Gnomad AFR AF: 0.0125

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00627

Gnomad ASJ AF: 0.00204

Gnomad EAS AF: 0.00570

Gnomad SAS AF: 0.0111

Gnomad FIN AF: 0.0236

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0171

Gnomad OTH AF: 0.0101

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

GnomAD4 genome AF: 0.0141 AC: 2062 AN: 146288 Hom.: 18 Cov.: 0 AF XY: 0.0144 AC XY: 1026 AN XY: 71036

Gnomad4 AFR AF: 0.0127

Gnomad4 AMR AF: 0.00626

Gnomad4 ASJ AF: 0.00204

Gnomad4 EAS AF: 0.00551

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.0236

Gnomad4 NFE AF: 0.0171

Gnomad4 OTH AF: 0.0105

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3222967; hg19: chr7-142007188;