rs7146962

Positions:

• chr14-53678599-T-C

Variant summary

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

The ENST00000648066.1(ENSG00000237356):​n.335-8600T>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 0.301 in 152,096 control chromosomes in the GnomAD database, including 7,437 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 0.30 (7437 hom., cov: 32)
• Consequence: ENST00000648066.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370504	XR_943876.3	n.29701-8600T>C		intron_variant, non_coding_transcript_variant
LOC105370504	XR_001750974.1	n.3896-8600T>C		intron_variant, non_coding_transcript_variant
LOC105370504	XR_001750975.3	n.29701-8600T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648066.1	n.335-8600T>C		intron_variant, non_coding_transcript_variant
	ENST00000456100.6	n.326-8600T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000663444.1	n.560-8600T>C		intron_variant, non_coding_transcript_variant
	ENST00000669612.1	n.398-8600T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45644 AN: 151978 Hom.: 7403 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.301 AC: 45744 AN: 152096 Hom.: 7437 Cov.: 32 AF XY: 0.296 AC XY: 22006 AN XY: 74352

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.307

Alfa AF: 0.266 Hom.: 2744

Bravo AF: 0.317

Asia WGS AF: 0.307 AC: 1067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.19
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7146962; hg19: chr14-54145317;