rs6478338

Positions:

• chr9-117945495-T-C

Variant summary

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

The ENST00000697639.1(ENSG00000284977):​n.1053+97340T>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 0.201 in 152,058 control chromosomes in the GnomAD database, including 3,346 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 0.20 (3346 hom., cov: 32)
• Consequence: ENST00000697639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000697639.1	n.1053+97340T>C		intron_variant, non_coding_transcript_variant
	ENST00000697724.1	n.1173-111535T>C		intron_variant, non_coding_transcript_variant
	ENST00000703416.1	n.346+97340T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30608 AN: 151940 Hom.: 3345 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.201 AC: 30622 AN: 152058 Hom.: 3346 Cov.: 32 AF XY: 0.198 AC XY: 14698 AN XY: 74324

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.200

Alfa AF: 0.191 Hom.: 597

Bravo AF: 0.205

Asia WGS AF: 0.219 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6478338; hg19: chr9-120707773;