chr2-78230615-G-T

Position:

• chr2-78230615-G-T

Variant summary

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

The NR_110288.1(LOC101927967):​n.344+59773C>A 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 0.141 in 151,812 control chromosomes in the GnomAD database, including 3,565 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 0.14 (3565 hom., cov: 32)
• Consequence: LOC101927967 NR_110288.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927967	NR_110288.1	n.344+59773C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000667782.1	n.82+59773C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21401 AN: 151696 Hom.: 3556 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.0665

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0154

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0370

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.141 AC: 21435 AN: 151812 Hom.: 3565 Cov.: 32 AF XY: 0.135 AC XY: 10019 AN XY: 74204

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.0831

Gnomad4 ASJ AF: 0.0665

Gnomad4 EAS AF: 0.000971

Gnomad4 SAS AF: 0.0268

Gnomad4 FIN AF: 0.0154

Gnomad4 NFE AF: 0.0370

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0462 Hom.: 428

Bravo AF: 0.158

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6547194; hg19: chr2-78457741;