rs7805622

chr7-56483270-A-Gchr7-56483270-A-T

Variant summary

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

The NR_108095.1(LOC100240728):n.50T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,266 control chromosomes in the GnomAD database, including 55,701 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 0.85 (55666 hom., cov: 31)
  • Exomes 𝑓: 0.84 (35 hom.)
• Consequence: LOC100240728 NR_108095.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100240728	NR_108095.1	n.50T>C		non_coding_transcript_exon_variant	1/2
LOC124901640	XR_007060331.1	n.148A>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000666625.1	n.1117T>C		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129494 AN: 152050 Hom.: 55611 Cov.: 31

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.862

GnomAD4 exome AF: 0.837 AC: 82 AN: 98 Hom.: 35 Cov.: 0 AF XY: 0.803 AC XY: 53 AN XY: 66

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.667

Gnomad4 NFE exome AF: 0.911

Gnomad4 OTH exome AF: 0.900

GnomAD4 genome AF: 0.852 AC: 129604 AN: 152168 Hom.: 55666 Cov.: 31 AF XY: 0.848 AC XY: 63097 AN XY: 74386

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.888

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.862

Alfa AF: 0.828 Hom.: 85209

Bravo AF: 0.865

Asia WGS AF: 0.783 AC: 2722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	6.1
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7805622; hg19: chr7-56550963;