rs7963343

Positions:

• chr12-93901846-T-G

Variant summary

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

The NR_135017.1(LOC105369911):​n.143-6481A>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 0.168 in 152,184 control chromosomes in the GnomAD database, including 2,281 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 0.17 (2281 hom., cov: 32)
• Consequence: LOC105369911 NR_135017.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369911	NR_135017.1	n.143-6481A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000550687.1	n.140-6481A>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25580 AN: 152066 Hom.: 2273 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.168 AC: 25608 AN: 152184 Hom.: 2281 Cov.: 32 AF XY: 0.169 AC XY: 12550 AN XY: 74426

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.0391

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.150

Alfa AF: 0.170 Hom.: 1080

Bravo AF: 0.170

Asia WGS AF: 0.0870 AC: 302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7963343; hg19: chr12-94295622;