rs12685977

Positions:

• chr9-111236635-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000426204.1(ENSG00000227531):​n.370+36178T>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 0.0104 in 152,334 control chromosomes in the GnomAD database, including 19 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 0.010 (19 hom., cov: 32)
• Consequence: ENST00000426204.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0104 (1587/152334) while in subpopulation EAS AF= 0.0406 (211/5192). AF 95% confidence interval is 0.0361. There are 19 homozygotes in gnomad4. There are 830 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 19 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376219	XR_001746894.2	n.409+36178T>C		intron_variant, non_coding_transcript_variant
LOC105376219	XR_001746893.2	n.409+36178T>C		intron_variant, non_coding_transcript_variant
LOC105376219	XR_930247.3	n.409+36178T>C		intron_variant, non_coding_transcript_variant
LOC105376219	XR_930249.2	n.409+36178T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000426204.1	n.370+36178T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0104 AC: 1582 AN: 152216 Hom.: 19 Cov.: 32

Gnomad AFR AF: 0.0211

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0136

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.0404

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00144

Gnomad OTH AF: 0.0143

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

GnomAD4 genome AF: 0.0104 AC: 1587 AN: 152334 Hom.: 19 Cov.: 32 AF XY: 0.0111 AC XY: 830 AN XY: 74498

Gnomad4 AFR AF: 0.0212

Gnomad4 AMR AF: 0.0135

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.0406

Gnomad4 SAS AF: 0.0195

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00143

Gnomad4 OTH AF: 0.0142

Alfa AF: 0.00572 Hom.: 3

Bravo AF: 0.0117

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12685977; hg19: chr9-113998915;