chr16-64909123-T-A

Position:

• chr16-64909123-T-A

Variant summary

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

The XR_933677.2(LOC105371313):​n.116+574T>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 0.198 in 152,056 control chromosomes in the GnomAD database, including 3,506 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 0.20 (3506 hom., cov: 32)
• Consequence: LOC105371313 XR_933677.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646

Genes affected

LOC124903779 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903779	XR_007065223.1	n.121+1294A>T		intron_variant, non_coding_transcript_variant
LOC105371313	XR_933677.2	n.116+574T>A		intron_variant, non_coding_transcript_variant
LOC124903779	XR_007065222.1	n.165+1250A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30066 AN: 151938 Hom.: 3503 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.198 AC: 30091 AN: 152056 Hom.: 3506 Cov.: 32 AF XY: 0.206 AC XY: 15302 AN XY: 74302

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.192

Alfa AF: 0.0983 Hom.: 157

Bravo AF: 0.200

Asia WGS AF: 0.287 AC: 996 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500505; hg19: chr16-64943026;