7-27200863-C-G

Position:

• chr7-27200863-C-G

Variant summary

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

The ENST00000472494.1(HOTTIP):​n.326C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,586 control chromosomes in the GnomAD database, including 10,959 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 (10907 hom., cov: 32)
  • Exomes 𝑓: 0.41 (52 hom.)
• Consequence: HOTTIP ENST00000472494.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

Genes affected

HOTTIP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HOTTIP	NR_037843.3	n.342C>G		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HOTTIP	ENST00000421733.1	n.408C>G		non_coding_transcript_exon_variant	2/2	5
HOTTIP	ENST00000472494.1	n.326C>G		non_coding_transcript_exon_variant	2/2	2
HOTTIP	ENST00000605136.6	n.327C>G		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53315 AN: 151970 Hom.: 10904 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.397

GnomAD4 exome AF: 0.412 AC: 206 AN: 500 Hom.: 52 Cov.: 0 AF XY: 0.410 AC XY: 110 AN XY: 268

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 FIN exome AF: 0.416

Gnomad4 NFE exome AF: 0.390

Gnomad4 OTH exome AF: 0.409

GnomAD4 genome AF: 0.351 AC: 53323 AN: 152086 Hom.: 10907 Cov.: 32 AF XY: 0.349 AC XY: 25944 AN XY: 74336

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.402

Alfa AF: 0.392 Hom.: 1589

Bravo AF: 0.336

Asia WGS AF: 0.440 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3807598; hg19: chr7-27240482;