rs7021687

Positions:

• chr9-117765676-G-A
• chr9-117765676-G-T

Variant summary

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

The ENST00000697639.1(ENSG00000284977):​n.128-1422G>A 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 0.137 in 152,014 control chromosomes in the GnomAD database, including 3,635 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 0.14 (3635 hom., cov: 32)
• Consequence: ENST00000697639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376244	XR_007061905.1	n.1994-1422G>A		intron_variant, non_coding_transcript_variant
LOC105376244	XR_001746916.2	n.1235-1422G>A		intron_variant, non_coding_transcript_variant
LOC105376244	XR_007061906.1	n.1235-1422G>A		intron_variant, non_coding_transcript_variant
LOC105376244	XR_007061907.1	n.1994-1422G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000697639.1	n.128-1422G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20807 AN: 151896 Hom.: 3625 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.0973

Gnomad SAS AF: 0.0796

Gnomad FIN AF: 0.0495

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00884

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.137 AC: 20863 AN: 152014 Hom.: 3635 Cov.: 32 AF XY: 0.137 AC XY: 10204 AN XY: 74312

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.0971

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.0495

Gnomad4 NFE AF: 0.00885

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0238 Hom.: 58

Bravo AF: 0.154

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7021687; hg19: chr9-120527954;