rs7156227

Positions:

• chr14-53588619-A-G

Variant summary

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

The ENST00000648066.1(ENSG00000237356):​n.335-98580A>G 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 0.349 in 152,056 control chromosomes in the GnomAD database, including 9,377 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 0.35 (9377 hom., cov: 32)
• Consequence: ENST00000648066.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370504	XR_943876.3	n.29701-98580A>G		intron_variant, non_coding_transcript_variant
LOC105370504	XR_001750974.1	n.3896-98580A>G		intron_variant, non_coding_transcript_variant
LOC105370504	XR_001750975.3	n.29701-98580A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648066.1	n.335-98580A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53016 AN: 151938 Hom.: 9354 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.349 AC: 53081 AN: 152056 Hom.: 9377 Cov.: 32 AF XY: 0.346 AC XY: 25697 AN XY: 74318

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.327

Alfa AF: 0.336 Hom.: 17330

Bravo AF: 0.356

Asia WGS AF: 0.337 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7156227; hg19: chr14-54055337;