chr9-38375218-T-C

Position:

• chr9-38375218-T-C

Variant summary

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

The ENST00000422554.2(ENSG00000223716):​n.155-111T>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 0.715 in 152,188 control chromosomes in the GnomAD database, including 40,182 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 0.71 (40176 hom., cov: 32)
  • Exomes 𝑓: 1.0 (6 hom.)
• Consequence: ENST00000422554.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987065	XR_001746670.2	n.368+2241T>C		intron_variant, non_coding_transcript_variant
LOC105376040	XR_929605.1	n.321+55A>G		intron_variant, non_coding_transcript_variant
LOC107987065	XR_001746668.2	n.369-76T>C		intron_variant, non_coding_transcript_variant
LOC107987065	XR_001746669.2	n.269-76T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000422554.2	n.155-111T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108716 AN: 152056 Hom.: 40145 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.746

GnomAD4 exome AF: 1.00 AC: 12 AN: 12 Hom.: 6 AF XY: 1.00 AC XY: 8 AN XY: 8

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.715 AC: 108799 AN: 152176 Hom.: 40176 Cov.: 32 AF XY: 0.719 AC XY: 53527 AN XY: 74396

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.841

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.747

Alfa AF: 0.764 Hom.: 14054

Bravo AF: 0.704

Asia WGS AF: 0.780 AC: 2712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs987187; hg19: chr9-38375215;